Quality|quality|JJ|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 1.1.2|1.1.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-2|1-2|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Read|Read|NNP|_ counting|count|VBG|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ the|the|DT|_ middle|middle|JJ|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|read|VB|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ unique|unique|JJ|_ CDS|cds|NN|_ per|per|IN|_ kilobase|kilobase|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPM|rpm|NN|_ -RRB-|-rrb-|-RRB-|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRI|TRI|NNP|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ enriched|enrich|VBN|_ by|by|IN|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|GeneJET|NNP|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ rRNA|rrna|NN|_ with|with|IN|_ MICROBExpres|microbexpre|NNS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ fragmented|fragmented|JJ|_ in|in|IN|_ alkaline|alkaline|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ and|and|CC|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ pH|ph|NN|_ 9.2|9.2|CD|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ fragments|fragment|NNS|_ with|with|IN|_ size|size|NN|_ of|of|IN|_ 24-35|24-35|CD|_ nts|nt|NNS|_ .|.|.|_ For|for|IN|_ RPFS|rpf|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ freeze-rupturing|freeze-rupturing|NN|_ -LRB-|-lrb-|-LRB-|_ Retch|Retch|NNP|_ Mill|Mill|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 100|100|CD|_ A260|a260|NN|_ units|unit|NNS|_ of|of|IN|_ ribosome-bound|ribosome-bound|JJ|_ mRNA|mrna|NN|_ fraction|fraction|NN|_ were|be|VBD|_ directly|directly|RB|_ used|use|VBN|_ for|for|IN|_ polysomal|polysomal|JJ|_ analysis|analysis|NN|_ or|or|CC|_ subjected|subject|VBN|_ to|to|TO|_ nucleolytic|nucleolytic|JJ|_ digestion|digestion|NN|_ with|with|IN|_ 10|10|CD|_ units/µl|units/µl|NN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ in|in|IN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 9.2|9.2|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 11|11|CD|_ containing|contain|VBG|_ 50|50|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ triton|triton|NN|_ X-100|x-100|NN|_ ,|,|,|_ 100|100|CD|_ µg/ml|µg/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ and|and|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ obtain|obtain|VB|_ the|the|DT|_ monosomal|monosomal|JJ|_ fraction|fraction|NN|_ .|.|.|_ Separation|separation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ sucrose|sucrose|NN|_ density|density|NN|_ gradient|gradient|NN|_ -LRB-|-lrb-|-LRB-|_ 15-50|15-50|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ 20-35-nt|20-35-nt|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ from|from|IN|_ the|the|DT|_ monosomal|monosomal|JJ|_ fraction|fraction|NN|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ on|on|IN|_ a|a|DT|_ denaturing|denature|VBG|_ 15|15|CD|_ %|%|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ .|.|.|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ Difco|Difco|NNP|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg/ml|µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ single|single|JJ|_ fresh|fresh|JJ|_ grown|grown|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.03|0.03|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ MG1693|mg1693|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|exponential|JJ|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ Difco|Difco|NNP|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg/ml|µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ single|single|JJ|_ fresh|fresh|JJ|_ grown|grown|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.03|0.03|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ MG1693|mg1693|NN|_
Irina|Irina|NNP|_ ,|,|,|_ ,|,|,|_ Chelysheva|Chelysheva|NNP|_
Quality|Quality|NNP|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 1.1.2|1.1.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-2|1-2|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Read|Read|NNP|_ counting|count|VBG|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ the|the|DT|_ middle|middle|JJ|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|read|VB|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ unique|unique|JJ|_ CDS|cds|NN|_ per|per|IN|_ kilobase|kilobase|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPM|rpm|NN|_ -RRB-|-rrb-|-RRB-|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRI|TRI|NNP|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ enriched|enrich|VBN|_ by|by|IN|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|GeneJET|NNP|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ rRNA|rrna|NN|_ with|with|IN|_ MICROBExpres|microbexpre|NNS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ fragmented|fragmented|JJ|_ in|in|IN|_ alkaline|alkaline|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ and|and|CC|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ pH|ph|NN|_ 9.2|9.2|CD|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ fragments|fragment|NNS|_ with|with|IN|_ size|size|NN|_ of|of|IN|_ 24-35|24-35|CD|_ nts|nt|NNS|_ .|.|.|_ For|for|IN|_ RPFS|rpf|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ freeze-rupturing|freeze-rupturing|NN|_ -LRB-|-lrb-|-LRB-|_ Retch|Retch|NNP|_ Mill|Mill|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 100|100|CD|_ A260|a260|NN|_ units|unit|NNS|_ of|of|IN|_ ribosome-bound|ribosome-bound|JJ|_ mRNA|mrna|NN|_ fraction|fraction|NN|_ were|be|VBD|_ directly|directly|RB|_ used|use|VBN|_ for|for|IN|_ polysomal|polysomal|JJ|_ analysis|analysis|NN|_ or|or|CC|_ subjected|subject|VBN|_ to|to|TO|_ nucleolytic|nucleolytic|JJ|_ digestion|digestion|NN|_ with|with|IN|_ 10|10|CD|_ units/µl|units/µl|NN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ in|in|IN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 9.2|9.2|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 11|11|CD|_ containing|contain|VBG|_ 50|50|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ triton|triton|NN|_ X-100|x-100|NN|_ ,|,|,|_ 100|100|CD|_ µg/ml|µg/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ and|and|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ obtain|obtain|VB|_ the|the|DT|_ monosomal|monosomal|JJ|_ fraction|fraction|NN|_ .|.|.|_ Separation|separation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ sucrose|sucrose|NN|_ density|density|NN|_ gradient|gradient|NN|_ -LRB-|-lrb-|-LRB-|_ 15-50|15-50|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ 20-35-nt|20-35-nt|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ from|from|IN|_ the|the|DT|_ monosomal|monosomal|JJ|_ fraction|fraction|NN|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ on|on|IN|_ a|a|DT|_ denaturing|denature|VBG|_ 15|15|CD|_ %|%|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ .|.|.|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ Difco|Difco|NNP|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg/ml|µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ single|single|JJ|_ fresh|fresh|JJ|_ grown|grown|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.03|0.03|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ CMA540|cma540|NN|_ -LRB-|-lrb-|-LRB-|_ MG1693|mg1693|NN|_ ∆|∆|CD|_ hfq|hfq|NN|GEN :|:|:|_ :|:|:|_ cat|cat|NN|_ -RRB-|-rrb-|-RRB-|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CMA540|cma540|NN|_ -LRB-|-lrb-|-LRB-|_ MG1693|mg1693|NN|_ delta|delta|NN|_ _|_|NN|_ hfq|hfq|NN|GEN :|:|:|_ :|:|:|_ cat|cat|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|exponential|JJ|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ Difco|Difco|NNP|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg/ml|µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ single|single|JJ|_ fresh|fresh|JJ|_ grown|grown|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.03|0.03|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ CMA540|cma540|NN|_ -LRB-|-lrb-|-LRB-|_ MG1693|mg1693|NN|_ ∆|∆|CD|_ hfq|hfq|NN|GEN :|:|:|_ :|:|:|_ cat|cat|NN|_ -RRB-|-rrb-|-RRB-|_
Irina|Irina|NNP|_ ,|,|,|_ ,|,|,|_ Chelysheva|Chelysheva|NNP|_
Quality|Quality|NNP|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 1.1.2|1.1.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-2|1-2|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Read|Read|NNP|_ counting|count|VBG|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ the|the|DT|_ middle|middle|JJ|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|read|VB|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ unique|unique|JJ|_ CDS|cds|NN|_ per|per|IN|_ kilobase|kilobase|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPM|rpm|NN|_ -RRB-|-rrb-|-RRB-|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRI|TRI|NNP|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ enriched|enrich|VBN|_ by|by|IN|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|GeneJET|NNP|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ rRNA|rrna|NN|_ with|with|IN|_ MICROBExpres|microbexpre|NNS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ fragmented|fragmented|JJ|_ in|in|IN|_ alkaline|alkaline|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ and|and|CC|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ pH|ph|NN|_ 9.2|9.2|CD|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ fragments|fragment|NNS|_ with|with|IN|_ size|size|NN|_ of|of|IN|_ 24-35|24-35|CD|_ nts|nt|NNS|_ .|.|.|_ For|for|IN|_ RPFS|rpf|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ freeze-rupturing|freeze-rupturing|NN|_ -LRB-|-lrb-|-LRB-|_ Retch|Retch|NNP|_ Mill|Mill|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 100|100|CD|_ A260|a260|NN|_ units|unit|NNS|_ of|of|IN|_ ribosome-bound|ribosome-bound|JJ|_ mRNA|mrna|NN|_ fraction|fraction|NN|_ were|be|VBD|_ directly|directly|RB|_ used|use|VBN|_ for|for|IN|_ polysomal|polysomal|JJ|_ analysis|analysis|NN|_ or|or|CC|_ subjected|subject|VBN|_ to|to|TO|_ nucleolytic|nucleolytic|JJ|_ digestion|digestion|NN|_ with|with|IN|_ 10|10|CD|_ units/µl|units/µl|NN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ in|in|IN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 9.2|9.2|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 11|11|CD|_ containing|contain|VBG|_ 50|50|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ triton|triton|NN|_ X-100|x-100|NN|_ ,|,|,|_ 100|100|CD|_ µg/ml|µg/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ and|and|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ obtain|obtain|VB|_ the|the|DT|_ monosomal|monosomal|JJ|_ fraction|fraction|NN|_ .|.|.|_ Separation|separation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ sucrose|sucrose|NN|_ density|density|NN|_ gradient|gradient|NN|_ -LRB-|-lrb-|-LRB-|_ 15-50|15-50|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ 20-35-nt|20-35-nt|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ from|from|IN|_ the|the|DT|_ monosomal|monosomal|JJ|_ fraction|fraction|NN|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ on|on|IN|_ a|a|DT|_ denaturing|denature|VBG|_ 15|15|CD|_ %|%|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ .|.|.|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ Difco|Difco|NNP|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg/ml|µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ single|single|JJ|_ fresh|fresh|JJ|_ grown|grown|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.03|0.03|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ MG1693|mg1693|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|exponential|JJ|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ Difco|Difco|NNP|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg/ml|µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ single|single|JJ|_ fresh|fresh|JJ|_ grown|grown|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.03|0.03|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ MG1693|mg1693|NN|_
Irina|Irina|NNP|_ ,|,|,|_ ,|,|,|_ Chelysheva|Chelysheva|NNP|_
Quality|Quality|NNP|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 1.1.2|1.1.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-2|1-2|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Read|Read|NNP|_ counting|count|VBG|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ the|the|DT|_ middle|middle|JJ|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|read|VB|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ unique|unique|JJ|_ CDS|cds|NN|_ per|per|IN|_ kilobase|kilobase|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPM|rpm|NN|_ -RRB-|-rrb-|-RRB-|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRI|TRI|NNP|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ enriched|enrich|VBN|_ by|by|IN|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|GeneJET|NNP|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ rRNA|rrna|NN|_ with|with|IN|_ MICROBExpres|microbexpre|NNS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ fragmented|fragmented|JJ|_ in|in|IN|_ alkaline|alkaline|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ and|and|CC|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ pH|ph|NN|_ 9.2|9.2|CD|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ fragments|fragment|NNS|_ with|with|IN|_ size|size|NN|_ of|of|IN|_ 24-35|24-35|CD|_ nts|nt|NNS|_ .|.|.|_ For|for|IN|_ RPFS|rpf|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ freeze-rupturing|freeze-rupturing|NN|_ -LRB-|-lrb-|-LRB-|_ Retch|Retch|NNP|_ Mill|Mill|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 100|100|CD|_ A260|a260|NN|_ units|unit|NNS|_ of|of|IN|_ ribosome-bound|ribosome-bound|JJ|_ mRNA|mrna|NN|_ fraction|fraction|NN|_ were|be|VBD|_ directly|directly|RB|_ used|use|VBN|_ for|for|IN|_ polysomal|polysomal|JJ|_ analysis|analysis|NN|_ or|or|CC|_ subjected|subject|VBN|_ to|to|TO|_ nucleolytic|nucleolytic|JJ|_ digestion|digestion|NN|_ with|with|IN|_ 10|10|CD|_ units/µl|units/µl|NN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ in|in|IN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 9.2|9.2|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 11|11|CD|_ containing|contain|VBG|_ 50|50|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ triton|triton|NN|_ X-100|x-100|NN|_ ,|,|,|_ 100|100|CD|_ µg/ml|µg/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ and|and|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ obtain|obtain|VB|_ the|the|DT|_ monosomal|monosomal|JJ|_ fraction|fraction|NN|_ .|.|.|_ Separation|separation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ sucrose|sucrose|NN|_ density|density|NN|_ gradient|gradient|NN|_ -LRB-|-lrb-|-LRB-|_ 15-50|15-50|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ 20-35-nt|20-35-nt|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ from|from|IN|_ the|the|DT|_ monosomal|monosomal|JJ|_ fraction|fraction|NN|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ on|on|IN|_ a|a|DT|_ denaturing|denature|VBG|_ 15|15|CD|_ %|%|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ .|.|.|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ Difco|Difco|NNP|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg/ml|µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ single|single|JJ|_ fresh|fresh|JJ|_ grown|grown|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.03|0.03|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ CMA540|cma540|NN|_ -LRB-|-lrb-|-LRB-|_ MG1693|mg1693|NN|_ ∆|∆|CD|_ hfq|hfq|NN|GEN :|:|:|_ :|:|:|_ cat|cat|NN|_ -RRB-|-rrb-|-RRB-|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CMA540|cma540|NN|_ -LRB-|-lrb-|-LRB-|_ MG1693|mg1693|NN|_ delta|delta|NN|_ _|_|NN|_ hfq|hfq|NN|GEN :|:|:|_ :|:|:|_ cat|cat|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|exponential|JJ|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ Difco|Difco|NNP|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg/ml|µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ single|single|JJ|_ fresh|fresh|JJ|_ grown|grown|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.03|0.03|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ appr|appr|NN|_ .|.|.|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ CMA540|cma540|NN|_ -LRB-|-lrb-|-LRB-|_ MG1693|mg1693|NN|_ ∆|∆|CD|_ hfq|hfq|NN|GEN :|:|:|_ :|:|:|_ cat|cat|NN|_ -RRB-|-rrb-|-RRB-|_
Irina|Irina|NNP|_ ,|,|,|_ ,|,|,|_ Chelysheva|Chelysheva|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspABEG|cspabeg|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ cspABEG|cspabeg|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspABEG|cspabeg|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspABCEG|cspabceg|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ cspABCEG|cspabceg|NN|_
temperature|temperature|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspABCEG|cspabceg|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspABEG|cspabeg|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ cspABEG|cspabeg|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspABEG|cspabeg|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ DMS-modified|dms-modified|JJ|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ DMS-modified|dms-modified|JJ|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ DMS-modified|dms-modified|JJ|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspABEG|cspabeg|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ cspABEG|cspabeg|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ DMS-modified|dms-modified|JJ|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspABEG|cspabeg|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspBG|cspbg|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ cspBG|cspbg|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ DMS-modified|dms-modified|JJ|_ mRNA|mrna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspBG|cspbg|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ rnr|rnr|NN|GEN
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ rnr|rnr|NN|GEN
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ rnr|rnr|NN|GEN
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
treatment|treatment|NN|_ :|:|:|_ Before|before|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
treatment|treatment|NN|_ :|:|:|_ After|after|IN|_ 250|250|CD|_ µg/mL|µg/ml|NN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ for|for|IN|_ 2|2|CD|_ hr|hr|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ rnr|rnr|NN|GEN
treatment|treatment|NN|_ :|:|:|_ Before|before|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ rnr|rnr|NN|GEN
treatment|treatment|NN|_ :|:|:|_ After|after|IN|_ 250|250|CD|_ µg/mL|µg/ml|NN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ for|for|IN|_ 2|2|CD|_ hr|hr|NN|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13519|gj13519|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13519|gj13519|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13519|gj13519|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13519|gj13519|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13519|gj13519|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13519|gj13519|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13533|gj13533|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13533|gj13533|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13533|gj13533|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13531|gj13531|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ rho|rho|NN|GEN
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13531|gj13531|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ rho|rho|NN|GEN
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13531|gj13531|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ rho|rho|NN|GEN
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13507|gj13507|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ nusG|nusg|NN|GEN
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13507|gj13507|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ nusG|nusg|NN|GEN
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
ssRNA-seq|ssrna-seq|JJ|_
substrain|substrain|NN|_ :|:|:|_ GJ13507|gj13507|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ nusG|nusg|NN|GEN
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531/pHYD2411|gj13531/phyd2411|NN|_ and|and|CC|_ GJ13507|gj13507|NN|_ /|/|:|_ pHYD2412|phyd2412|NN|_ on|on|IN|_ glucose-minimal|glucose-minimal|NN|_ A|a|NN|_ plates|plate|VBZ|_ supplemented|supplement|VBN|_ with|with|IN|_ Xgal|xgal|NN|_ and|and|CC|_ IPTG|iptg|NN|_ at|at|IN|_ 200|200|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ μM|μm|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
J|j|NN|_ ,|,|,|_ ,|,|,|_ Gowrishankar|Gowrishankar|NNP|_
Raw|raw|NN|_ .|.|.|_ fastq|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BWA|bwa|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.7|0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ to|to|TO|_ read|read|VB|_ count|count|NN|_ per|per|IN|_ gene|gene|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ the|the|DT|_ case|case|NN|_ of|of|IN|_ Ion|ion|NN|_ torrent|torrent|NN|_ data|datum|NNS|_ .|.|.|_ bam|bam|NN|_ files|file|NNS|_ were|be|VBD|_ converted|convert|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ .|.|.|_
Resulting|Resulting|NNP|_ read|read|VBD|_ count|count|NN|_ matrix|matrix|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ for|for|IN|_ the|the|DT|_ differntial|differntial|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ in|in|IN|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.12.1|3.12.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ -LRB-|-lrb-|-LRB-|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ values|value|NNS|_ ,|,|,|_ p-values|p-value|NNS|_ -RRB-|-rrb-|-RRB-|_
NEXTflexRapid|nextflexrapid|NN|_ Directional|directional|JJ|_ RNA-Seq|rna-seq|NN|_ library|library|NN|_ kit|kit|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1657|mg1657|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Early|early|JJ|_ exponential|exponential|JJ|_
genotype|genotype|NN|_ :|:|:|_ fis|fis|NN|GEN mutant|mutant|JJ|_ background|background|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
Parul|Parul|NNP|_ ,|,|,|_ ,|,|,|_ Singh|Singh|NNP|_
Raw|raw|NN|_ .|.|.|_ fastq|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BWA|bwa|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.7|0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ to|to|TO|_ read|read|VB|_ count|count|NN|_ per|per|IN|_ gene|gene|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ the|the|DT|_ case|case|NN|_ of|of|IN|_ Ion|ion|NN|_ torrent|torrent|NN|_ data|datum|NNS|_ .|.|.|_ bam|bam|NN|_ files|file|NNS|_ were|be|VBD|_ converted|convert|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ .|.|.|_
Resulting|Resulting|NNP|_ read|read|VBD|_ count|count|NN|_ matrix|matrix|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ for|for|IN|_ the|the|DT|_ differntial|differntial|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ in|in|IN|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.12.1|3.12.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ -LRB-|-lrb-|-LRB-|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ values|value|NNS|_ ,|,|,|_ p-values|p-value|NNS|_ -RRB-|-rrb-|-RRB-|_
NEXTflexRapid|nextflexrapid|NN|_ Directional|directional|JJ|_ RNA-Seq|rna-seq|NN|_ library|library|NN|_ kit|kit|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1667|mg1667|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Mid|Mid|NNP|_ exponential|exponential|JJ|_
genotype|genotype|NN|_ :|:|:|_ fis|fis|NN|GEN mutant|mutant|JJ|_ background|background|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
Parul|Parul|NNP|_ ,|,|,|_ ,|,|,|_ Singh|Singh|NNP|_
Raw|raw|NN|_ .|.|.|_ fastq|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BWA|bwa|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.7|0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ to|to|TO|_ read|read|VB|_ count|count|NN|_ per|per|IN|_ gene|gene|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ the|the|DT|_ case|case|NN|_ of|of|IN|_ Ion|ion|NN|_ torrent|torrent|NN|_ data|datum|NNS|_ .|.|.|_ bam|bam|NN|_ files|file|NNS|_ were|be|VBD|_ converted|convert|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ .|.|.|_
Resulting|Resulting|NNP|_ read|read|VBD|_ count|count|NN|_ matrix|matrix|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ for|for|IN|_ the|the|DT|_ differntial|differntial|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ in|in|IN|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.12.1|3.12.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ -LRB-|-lrb-|-LRB-|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ values|value|NNS|_ ,|,|,|_ p-values|p-value|NNS|_ -RRB-|-rrb-|-RRB-|_
NEXTflexRapid|nextflexrapid|NN|_ Directional|directional|JJ|_ RNA-Seq|rna-seq|NN|_ library|library|NN|_ kit|kit|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1668|mg1668|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Mid|Mid|NNP|_ exponential|exponential|JJ|_
genotype|genotype|NN|_ :|:|:|_ fis|fis|NN|GEN mutant|mutant|JJ|_ background|background|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
Parul|Parul|NNP|_ ,|,|,|_ ,|,|,|_ Singh|Singh|NNP|_
Raw|raw|NN|_ .|.|.|_ fastq|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BWA|bwa|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.7|0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ to|to|TO|_ read|read|VB|_ count|count|NN|_ per|per|IN|_ gene|gene|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ the|the|DT|_ case|case|NN|_ of|of|IN|_ Ion|ion|NN|_ torrent|torrent|NN|_ data|datum|NNS|_ .|.|.|_ bam|bam|NN|_ files|file|NNS|_ were|be|VBD|_ converted|convert|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ .|.|.|_
Resulting|Resulting|NNP|_ read|read|VBD|_ count|count|NN|_ matrix|matrix|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ for|for|IN|_ the|the|DT|_ differntial|differntial|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ in|in|IN|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.12.1|3.12.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ -LRB-|-lrb-|-LRB-|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ values|value|NNS|_ ,|,|,|_ p-values|p-value|NNS|_ -RRB-|-rrb-|-RRB-|_
NEXTflexRapid|nextflexrapid|NN|_ Directional|directional|JJ|_ RNA-Seq|rna-seq|NN|_ library|library|NN|_ kit|kit|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1672|mg1672|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Mid|Mid|NNP|_ exponential|exponential|JJ|_
genotype|genotype|NN|_ :|:|:|_ cya|cya|NN|_ mutant|mutant|JJ|_ background|background|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
Parul|Parul|NNP|_ ,|,|,|_ ,|,|,|_ Singh|Singh|NNP|_
Raw|raw|NN|_ .|.|.|_ fastq|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BWA|bwa|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.7|0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ to|to|TO|_ read|read|VB|_ count|count|NN|_ per|per|IN|_ gene|gene|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ the|the|DT|_ case|case|NN|_ of|of|IN|_ Ion|ion|NN|_ torrent|torrent|NN|_ data|datum|NNS|_ .|.|.|_ bam|bam|NN|_ files|file|NNS|_ were|be|VBD|_ converted|convert|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ .|.|.|_
Resulting|Resulting|NNP|_ read|read|VBD|_ count|count|NN|_ matrix|matrix|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ for|for|IN|_ the|the|DT|_ differntial|differntial|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ in|in|IN|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.12.1|3.12.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ -LRB-|-lrb-|-LRB-|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ values|value|NNS|_ ,|,|,|_ p-values|p-value|NNS|_ -RRB-|-rrb-|-RRB-|_
NEXTflexRapid|nextflexrapid|NN|_ Directional|directional|JJ|_ RNA-Seq|rna-seq|NN|_ library|library|NN|_ kit|kit|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1673|mg1673|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Mid|Mid|NNP|_ exponential|exponential|JJ|_
genotype|genotype|NN|_ :|:|:|_ wildtype|wildtype|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
Parul|Parul|NNP|_ ,|,|,|_ ,|,|,|_ Singh|Singh|NNP|_
Raw|raw|NN|_ .|.|.|_ fastq|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BWA|bwa|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.7|0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ to|to|TO|_ read|read|VB|_ count|count|NN|_ per|per|IN|_ gene|gene|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ the|the|DT|_ case|case|NN|_ of|of|IN|_ Ion|ion|NN|_ torrent|torrent|NN|_ data|datum|NNS|_ .|.|.|_ bam|bam|NN|_ files|file|NNS|_ were|be|VBD|_ converted|convert|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ .|.|.|_
Resulting|Resulting|NNP|_ read|read|VBD|_ count|count|NN|_ matrix|matrix|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ for|for|IN|_ the|the|DT|_ differntial|differntial|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ in|in|IN|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.12.1|3.12.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ -LRB-|-lrb-|-LRB-|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ values|value|NNS|_ ,|,|,|_ p-values|p-value|NNS|_ -RRB-|-rrb-|-RRB-|_
NEXTflexRapid|nextflexrapid|NN|_ Directional|directional|JJ|_ RNA-Seq|rna-seq|NN|_ library|library|NN|_ kit|kit|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1674|mg1674|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Mid|Mid|NNP|_ exponential|exponential|JJ|_
genotype|genotype|NN|_ :|:|:|_ wildtype|wildtype|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
cells|cell|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
Parul|Parul|NNP|_ ,|,|,|_ ,|,|,|_ Singh|Singh|NNP|_
We|we|PRP|_ used|use|VBD|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ and|and|CC|_ a|a|DT|_ MID|mid|NN|_ 150|150|CD|_ Kit|kit|NN|_ with|with|IN|_ 1x75|1x75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_ Base-calling|base-calling|NN|_ was|be|VBD|_ perform|perform|VB|_ online|online|NN|_ during|during|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ procedure|procedure|NN|_ with|with|IN|_ the|the|DT|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ version|version|NN|_ 2.4.11|2.4.11|CD|_ and|and|CC|_ System|System|NNP|_ Suite|Suite|NNP|_ Version|Version|NNP|_ 2.1.2.1|2.1.2.1|CD|_ .|.|.|_
Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ instruments|instrument|NNS|_ generate|generate|VBP|_ per-cycle|per-cycle|JJ|_ BCL|BCL|NNP|_ base|base|NN|_ call|call|NN|_ files|file|NNS|_ as|as|IN|_ primary|primary|JJ|_ sequencing|sequencing|NN|_ output|output|NN|_ in|in|IN|_ bcl2|bcl2|NN|_ format|format|NN|_ .|.|.|_ Conversion|conversion|NN|_ of|of|IN|_ the|the|DT|_ bcl2|bcl2|NN|_ file|file|NN|_ to|to|TO|_ gzipped|gzipped|JJ|_ fastq|fastq|NN|_ files|file|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ bcl2fastq|bcl2fastq|NN|_ script|script|NN|_ v.|v.|CC|_ 2.18.0.12|2.18.0.12|CD|_ provided|provide|VBN|_ by|by|IN|_ Illumina|Illumina|NNP|_ .|.|.|_
Quality|Quality|NNP|_ and|and|CC|_ adapter|adapter|NN|_ trimming|trim|VBG|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ software|software|NN|_ package|package|NN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Trim|trim|VBP|_ Sequences|sequence|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
Mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ was|be|VBD|_ also|also|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Map|map|NN|_ Reads|read|VBZ|_ to|to|TO|_ Reference|Reference|NNP|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
For|for|IN|_ quantification|quantification|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ read|read|NN|_ counting|counting|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ alignments|alignment|NNS|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ Genomics|Genomics|NNP|_ Workbench|Workbench|NNP|_ were|be|VBD|_ exported|export|VBN|_ in|in|IN|_ BAM|BAM|NNP|_ format|format|NN|_ .|.|.|_ Read|Read|NNP|_ counting|counting|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ FeatureCounts|FeatureCounts|NNP|_ v.|v.|CC|_ 1.5.0-p1|1.5.0-p1|CD|_ program|program|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ Level|Level|NNP|_ :|:|:|_ meta-feature|meta-feature|JJ|_ leve|leve|NN|_ .|.|.|_ Paired-end|paired-end|NN|_ :|:|:|_ no|no|DT|_ .|.|.|_ Strand|strand|VB|_ specific|specific|JJ|_ :|:|:|_ yes|yes|UH|_ .|.|.|_ Multimapping|multimapp|VBG|_ reads|read|VBZ|_ :|:|:|_ counted|count|VBN|_ -LRB-|-lrb-|-LRB-|_ as|as|IN|_ fractions|fraction|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Multi-overlapping|multi-overlapping|JJ|_ reads|read|VBZ|_ :|:|:|_ not|not|RB|_ counted|count|VBN|_ .|.|.|_ Overlapping|overlapping|JJ|_ bases|basis|NNS|_ :|:|:|_ 30|30|CD|_ .|.|.|_ Read|Read|NNP|_ orientations|orientation|NNS|_ :|:|:|_ fr|fr|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 017626.1|017626.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Strain-expression|strain-expression|NN|_ .|.|.|_ xlsx|xlsx|NN|_ archive|archive|NN|_ contains|contain|VBZ|_ expression|expression|NN|_ values|value|NNS|_ in|in|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Reads|read|NNS|_ Per|per|IN|_ Kb|kb|NN|_ exon|exon|NN|_ -LRB-|-lrb-|-LRB-|_ contig|contig|NN|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ Million|Million|NNP|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ Mortazavi|Mortazavi|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ .|.|.|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 621-8|621-8|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ can|can|MD|GEN be|be|VB|_ directly|directly|RB|_ compared|compare|VBN|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ -RRB-|-rrb-|-RRB-|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ mill|mill|NN|_ and|and|CC|_ the|the|DT|_ mirVana|mirvana|NN|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ including|include|VBG|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
From|from|IN|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ first-strand|first-strand|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ After|after|IN|_ fragmentation|fragmentation|NN|_ ,|,|,|_ the|the|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ in|in|IN|_ a|a|DT|_ strand|strand|NN|_ specific|specific|JJ|_ manner|manner|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ For|for|IN|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ ,|,|,|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ a|a|DT|_ 25:1|25:1|CD|_ ratio|ratio|NN|_ .|.|.|_ The|the|DT|_ library|library|NN|_ pool|pool|NN|_ was|be|VBD|_ fractionated|fractionate|VBN|_ in|in|IN|_ the|the|DT|_ size|size|NN|_ range|range|NN|_ of|of|IN|_ 250-500|250-500|CD|_ bp|bp|NN|_ using|use|VBG|_ a|a|DT|_ differential|differential|JJ|_ clean|clean|JJ|_ -|-|:|_ up|up|RP|_ with|with|IN|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ kit|kit|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ pool|pool|NN|_ was|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ using|use|VBG|_ 75|75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_
LB|LB|NNP|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
cell|cell|NN|_ pellets|pellet|NNS|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
cell|cell|NN|_ pellets|pellet|NNS|_
Mario|Mario|NNP|_ ,|,|,|_ ,|,|,|_ Huttener|Huttener|NNP|_ Queiroz|Queiroz|NNP|_
We|we|PRP|_ used|use|VBD|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ and|and|CC|_ a|a|DT|_ MID|mid|NN|_ 150|150|CD|_ Kit|kit|NN|_ with|with|IN|_ 1x75|1x75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_ Base-calling|base-calling|NN|_ was|be|VBD|_ perform|perform|VB|_ online|online|NN|_ during|during|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ procedure|procedure|NN|_ with|with|IN|_ the|the|DT|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ version|version|NN|_ 2.4.11|2.4.11|CD|_ and|and|CC|_ System|System|NNP|_ Suite|Suite|NNP|_ Version|Version|NNP|_ 2.1.2.1|2.1.2.1|CD|_ .|.|.|_
Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ instruments|instrument|NNS|_ generate|generate|VBP|_ per-cycle|per-cycle|JJ|_ BCL|BCL|NNP|_ base|base|NN|_ call|call|NN|_ files|file|NNS|_ as|as|IN|_ primary|primary|JJ|_ sequencing|sequencing|NN|_ output|output|NN|_ in|in|IN|_ bcl2|bcl2|NN|_ format|format|NN|_ .|.|.|_ Conversion|conversion|NN|_ of|of|IN|_ the|the|DT|_ bcl2|bcl2|NN|_ file|file|NN|_ to|to|TO|_ gzipped|gzipped|JJ|_ fastq|fastq|NN|_ files|file|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ bcl2fastq|bcl2fastq|NN|_ script|script|NN|_ v.|v.|CC|_ 2.18.0.12|2.18.0.12|CD|_ provided|provide|VBN|_ by|by|IN|_ Illumina|Illumina|NNP|_ .|.|.|_
Quality|Quality|NNP|_ and|and|CC|_ adapter|adapter|NN|_ trimming|trim|VBG|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ software|software|NN|_ package|package|NN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Trim|trim|VBP|_ Sequences|sequence|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
Mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ was|be|VBD|_ also|also|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Map|map|NN|_ Reads|read|VBZ|_ to|to|TO|_ Reference|Reference|NNP|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
For|for|IN|_ quantification|quantification|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ read|read|NN|_ counting|counting|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ alignments|alignment|NNS|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ Genomics|Genomics|NNP|_ Workbench|Workbench|NNP|_ were|be|VBD|_ exported|export|VBN|_ in|in|IN|_ BAM|BAM|NNP|_ format|format|NN|_ .|.|.|_ Read|Read|NNP|_ counting|counting|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ FeatureCounts|FeatureCounts|NNP|_ v.|v.|CC|_ 1.5.0-p1|1.5.0-p1|CD|_ program|program|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ Level|Level|NNP|_ :|:|:|_ meta-feature|meta-feature|JJ|_ leve|leve|NN|_ .|.|.|_ Paired-end|paired-end|NN|_ :|:|:|_ no|no|DT|_ .|.|.|_ Strand|strand|VB|_ specific|specific|JJ|_ :|:|:|_ yes|yes|UH|_ .|.|.|_ Multimapping|multimapp|VBG|_ reads|read|VBZ|_ :|:|:|_ counted|count|VBN|_ -LRB-|-lrb-|-LRB-|_ as|as|IN|_ fractions|fraction|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Multi-overlapping|multi-overlapping|JJ|_ reads|read|VBZ|_ :|:|:|_ not|not|RB|_ counted|count|VBN|_ .|.|.|_ Overlapping|overlapping|JJ|_ bases|basis|NNS|_ :|:|:|_ 30|30|CD|_ .|.|.|_ Read|Read|NNP|_ orientations|orientation|NNS|_ :|:|:|_ fr|fr|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 017626.1|017626.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Strain-expression|strain-expression|NN|_ .|.|.|_ xlsx|xlsx|NN|_ archive|archive|NN|_ contains|contain|VBZ|_ expression|expression|NN|_ values|value|NNS|_ in|in|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Reads|read|NNS|_ Per|per|IN|_ Kb|kb|NN|_ exon|exon|NN|_ -LRB-|-lrb-|-LRB-|_ contig|contig|NN|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ Million|Million|NNP|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ Mortazavi|Mortazavi|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ .|.|.|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 621-8|621-8|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ can|can|MD|GEN be|be|VB|_ directly|directly|RB|_ compared|compare|VBN|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ -RRB-|-rrb-|-RRB-|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ mill|mill|NN|_ and|and|CC|_ the|the|DT|_ mirVana|mirvana|NN|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ including|include|VBG|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
From|from|IN|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ first-strand|first-strand|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ After|after|IN|_ fragmentation|fragmentation|NN|_ ,|,|,|_ the|the|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ in|in|IN|_ a|a|DT|_ strand|strand|NN|_ specific|specific|JJ|_ manner|manner|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ For|for|IN|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ ,|,|,|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ a|a|DT|_ 25:1|25:1|CD|_ ratio|ratio|NN|_ .|.|.|_ The|the|DT|_ library|library|NN|_ pool|pool|NN|_ was|be|VBD|_ fractionated|fractionate|VBN|_ in|in|IN|_ the|the|DT|_ size|size|NN|_ range|range|NN|_ of|of|IN|_ 250-500|250-500|CD|_ bp|bp|NN|_ using|use|VBG|_ a|a|DT|_ differential|differential|JJ|_ clean|clean|JJ|_ -|-|:|_ up|up|RP|_ with|with|IN|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ kit|kit|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ pool|pool|NN|_ was|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ using|use|VBG|_ 75|75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_
LB|LB|NNP|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
cell|cell|NN|_ pellets|pellet|NNS|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ mutant|mutant|JJ|_ hhahha2|hhahha2|NN|_
LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
cell|cell|NN|_ pellets|pellet|NNS|_
Mario|Mario|NNP|_ ,|,|,|_ ,|,|,|_ Huttener|Huttener|NNP|_ Queiroz|Queiroz|NNP|_
We|we|PRP|_ used|use|VBD|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ and|and|CC|_ a|a|DT|_ MID|mid|NN|_ 150|150|CD|_ Kit|kit|NN|_ with|with|IN|_ 1x75|1x75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_ Base-calling|base-calling|NN|_ was|be|VBD|_ perform|perform|VB|_ online|online|NN|_ during|during|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ procedure|procedure|NN|_ with|with|IN|_ the|the|DT|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ version|version|NN|_ 2.4.11|2.4.11|CD|_ and|and|CC|_ System|System|NNP|_ Suite|Suite|NNP|_ Version|Version|NNP|_ 2.1.2.1|2.1.2.1|CD|_ .|.|.|_
Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ instruments|instrument|NNS|_ generate|generate|VBP|_ per-cycle|per-cycle|JJ|_ BCL|BCL|NNP|_ base|base|NN|_ call|call|NN|_ files|file|NNS|_ as|as|IN|_ primary|primary|JJ|_ sequencing|sequencing|NN|_ output|output|NN|_ in|in|IN|_ bcl2|bcl2|NN|_ format|format|NN|_ .|.|.|_ Conversion|conversion|NN|_ of|of|IN|_ the|the|DT|_ bcl2|bcl2|NN|_ file|file|NN|_ to|to|TO|_ gzipped|gzipped|JJ|_ fastq|fastq|NN|_ files|file|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ bcl2fastq|bcl2fastq|NN|_ script|script|NN|_ v.|v.|CC|_ 2.18.0.12|2.18.0.12|CD|_ provided|provide|VBN|_ by|by|IN|_ Illumina|Illumina|NNP|_ .|.|.|_
Quality|Quality|NNP|_ and|and|CC|_ adapter|adapter|NN|_ trimming|trim|VBG|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ software|software|NN|_ package|package|NN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Trim|trim|VBP|_ Sequences|sequence|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
Mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ was|be|VBD|_ also|also|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Map|map|NN|_ Reads|read|VBZ|_ to|to|TO|_ Reference|Reference|NNP|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
For|for|IN|_ quantification|quantification|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ read|read|NN|_ counting|counting|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ alignments|alignment|NNS|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ Genomics|Genomics|NNP|_ Workbench|Workbench|NNP|_ were|be|VBD|_ exported|export|VBN|_ in|in|IN|_ BAM|BAM|NNP|_ format|format|NN|_ .|.|.|_ Read|Read|NNP|_ counting|counting|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ FeatureCounts|FeatureCounts|NNP|_ v.|v.|CC|_ 1.5.0-p1|1.5.0-p1|CD|_ program|program|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ Level|Level|NNP|_ :|:|:|_ meta-feature|meta-feature|JJ|_ leve|leve|NN|_ .|.|.|_ Paired-end|paired-end|NN|_ :|:|:|_ no|no|DT|_ .|.|.|_ Strand|strand|VB|_ specific|specific|JJ|_ :|:|:|_ yes|yes|UH|_ .|.|.|_ Multimapping|multimapp|VBG|_ reads|read|VBZ|_ :|:|:|_ counted|count|VBN|_ -LRB-|-lrb-|-LRB-|_ as|as|IN|_ fractions|fraction|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Multi-overlapping|multi-overlapping|JJ|_ reads|read|VBZ|_ :|:|:|_ not|not|RB|_ counted|count|VBN|_ .|.|.|_ Overlapping|overlapping|JJ|_ bases|basis|NNS|_ :|:|:|_ 30|30|CD|_ .|.|.|_ Read|Read|NNP|_ orientations|orientation|NNS|_ :|:|:|_ fr|fr|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 017626.1|017626.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Strain-expression|strain-expression|NN|_ .|.|.|_ xlsx|xlsx|NN|_ archive|archive|NN|_ contains|contain|VBZ|_ expression|expression|NN|_ values|value|NNS|_ in|in|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Reads|read|NNS|_ Per|per|IN|_ Kb|kb|NN|_ exon|exon|NN|_ -LRB-|-lrb-|-LRB-|_ contig|contig|NN|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ Million|Million|NNP|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ Mortazavi|Mortazavi|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ .|.|.|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 621-8|621-8|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ can|can|MD|GEN be|be|VB|_ directly|directly|RB|_ compared|compare|VBN|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ -RRB-|-rrb-|-RRB-|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ mill|mill|NN|_ and|and|CC|_ the|the|DT|_ mirVana|mirvana|NN|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ including|include|VBG|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
From|from|IN|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ first-strand|first-strand|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ After|after|IN|_ fragmentation|fragmentation|NN|_ ,|,|,|_ the|the|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ in|in|IN|_ a|a|DT|_ strand|strand|NN|_ specific|specific|JJ|_ manner|manner|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ For|for|IN|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ ,|,|,|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ a|a|DT|_ 25:1|25:1|CD|_ ratio|ratio|NN|_ .|.|.|_ The|the|DT|_ library|library|NN|_ pool|pool|NN|_ was|be|VBD|_ fractionated|fractionate|VBN|_ in|in|IN|_ the|the|DT|_ size|size|NN|_ range|range|NN|_ of|of|IN|_ 250-500|250-500|CD|_ bp|bp|NN|_ using|use|VBG|_ a|a|DT|_ differential|differential|JJ|_ clean|clean|JJ|_ -|-|:|_ up|up|RP|_ with|with|IN|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ kit|kit|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ pool|pool|NN|_ was|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ using|use|VBG|_ 75|75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_
LB|LB|NNP|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
cell|cell|NN|_ pellets|pellet|NNS|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ mutant|mutant|JJ|_ hhs|hh|NNS|_
LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
cell|cell|NN|_ pellets|pellet|NNS|_
Mario|Mario|NNP|_ ,|,|,|_ ,|,|,|_ Huttener|Huttener|NNP|_ Queiroz|Queiroz|NNP|_
We|we|PRP|_ used|use|VBD|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ and|and|CC|_ a|a|DT|_ MID|mid|NN|_ 150|150|CD|_ Kit|kit|NN|_ with|with|IN|_ 1x75|1x75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_ Base-calling|base-calling|NN|_ was|be|VBD|_ perform|perform|VB|_ online|online|NN|_ during|during|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ procedure|procedure|NN|_ with|with|IN|_ the|the|DT|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ version|version|NN|_ 2.4.11|2.4.11|CD|_ and|and|CC|_ System|System|NNP|_ Suite|Suite|NNP|_ Version|Version|NNP|_ 2.1.2.1|2.1.2.1|CD|_ .|.|.|_
Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ instruments|instrument|NNS|_ generate|generate|VBP|_ per-cycle|per-cycle|JJ|_ BCL|BCL|NNP|_ base|base|NN|_ call|call|NN|_ files|file|NNS|_ as|as|IN|_ primary|primary|JJ|_ sequencing|sequencing|NN|_ output|output|NN|_ in|in|IN|_ bcl2|bcl2|NN|_ format|format|NN|_ .|.|.|_ Conversion|conversion|NN|_ of|of|IN|_ the|the|DT|_ bcl2|bcl2|NN|_ file|file|NN|_ to|to|TO|_ gzipped|gzipped|JJ|_ fastq|fastq|NN|_ files|file|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ bcl2fastq|bcl2fastq|NN|_ script|script|NN|_ v.|v.|CC|_ 2.18.0.12|2.18.0.12|CD|_ provided|provide|VBN|_ by|by|IN|_ Illumina|Illumina|NNP|_ .|.|.|_
Quality|Quality|NNP|_ and|and|CC|_ adapter|adapter|NN|_ trimming|trim|VBG|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ software|software|NN|_ package|package|NN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Trim|trim|VBP|_ Sequences|sequence|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
Mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ was|be|VBD|_ also|also|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Map|map|NN|_ Reads|read|VBZ|_ to|to|TO|_ Reference|Reference|NNP|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
For|for|IN|_ quantification|quantification|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ read|read|NN|_ counting|counting|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ alignments|alignment|NNS|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ Genomics|Genomics|NNP|_ Workbench|Workbench|NNP|_ were|be|VBD|_ exported|export|VBN|_ in|in|IN|_ BAM|BAM|NNP|_ format|format|NN|_ .|.|.|_ Read|Read|NNP|_ counting|counting|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ FeatureCounts|FeatureCounts|NNP|_ v.|v.|CC|_ 1.5.0-p1|1.5.0-p1|CD|_ program|program|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ Level|Level|NNP|_ :|:|:|_ meta-feature|meta-feature|JJ|_ leve|leve|NN|_ .|.|.|_ Paired-end|paired-end|NN|_ :|:|:|_ no|no|DT|_ .|.|.|_ Strand|strand|VB|_ specific|specific|JJ|_ :|:|:|_ yes|yes|UH|_ .|.|.|_ Multimapping|multimapp|VBG|_ reads|read|VBZ|_ :|:|:|_ counted|count|VBN|_ -LRB-|-lrb-|-LRB-|_ as|as|IN|_ fractions|fraction|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Multi-overlapping|multi-overlapping|JJ|_ reads|read|VBZ|_ :|:|:|_ not|not|RB|_ counted|count|VBN|_ .|.|.|_ Overlapping|overlapping|JJ|_ bases|basis|NNS|_ :|:|:|_ 30|30|CD|_ .|.|.|_ Read|Read|NNP|_ orientations|orientation|NNS|_ :|:|:|_ fr|fr|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 017626.1|017626.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Strain-expression|strain-expression|NN|_ .|.|.|_ xlsx|xlsx|NN|_ archive|archive|NN|_ contains|contain|VBZ|_ expression|expression|NN|_ values|value|NNS|_ in|in|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Reads|read|NNS|_ Per|per|IN|_ Kb|kb|NN|_ exon|exon|NN|_ -LRB-|-lrb-|-LRB-|_ contig|contig|NN|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ Million|Million|NNP|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ Mortazavi|Mortazavi|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ .|.|.|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 621-8|621-8|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ can|can|MD|GEN be|be|VB|_ directly|directly|RB|_ compared|compare|VBN|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ -RRB-|-rrb-|-RRB-|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ mill|mill|NN|_ and|and|CC|_ the|the|DT|_ mirVana|mirvana|NN|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ including|include|VBG|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
From|from|IN|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ first-strand|first-strand|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ After|after|IN|_ fragmentation|fragmentation|NN|_ ,|,|,|_ the|the|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ in|in|IN|_ a|a|DT|_ strand|strand|NN|_ specific|specific|JJ|_ manner|manner|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ For|for|IN|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ ,|,|,|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ a|a|DT|_ 25:1|25:1|CD|_ ratio|ratio|NN|_ .|.|.|_ The|the|DT|_ library|library|NN|_ pool|pool|NN|_ was|be|VBD|_ fractionated|fractionate|VBN|_ in|in|IN|_ the|the|DT|_ size|size|NN|_ range|range|NN|_ of|of|IN|_ 250-500|250-500|CD|_ bp|bp|NN|_ using|use|VBG|_ a|a|DT|_ differential|differential|JJ|_ clean|clean|JJ|_ -|-|:|_ up|up|RP|_ with|with|IN|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ kit|kit|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ pool|pool|NN|_ was|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ using|use|VBG|_ 75|75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_
LB|LB|NNP|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
cell|cell|NN|_ pellets|pellet|NNS|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ mutant|mutant|JJ|_ hns2|hns2|NN|_
LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
cell|cell|NN|_ pellets|pellet|NNS|_
Mario|Mario|NNP|_ ,|,|,|_ ,|,|,|_ Huttener|Huttener|NNP|_ Queiroz|Queiroz|NNP|_
We|we|PRP|_ used|use|VBD|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ and|and|CC|_ a|a|DT|_ MID|mid|NN|_ 150|150|CD|_ Kit|kit|NN|_ with|with|IN|_ 1x75|1x75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_ Base-calling|base-calling|NN|_ was|be|VBD|_ perform|perform|VB|_ online|online|NN|_ during|during|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ procedure|procedure|NN|_ with|with|IN|_ the|the|DT|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ version|version|NN|_ 2.4.11|2.4.11|CD|_ and|and|CC|_ System|System|NNP|_ Suite|Suite|NNP|_ Version|Version|NNP|_ 2.1.2.1|2.1.2.1|CD|_ .|.|.|_
Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ instruments|instrument|NNS|_ generate|generate|VBP|_ per-cycle|per-cycle|JJ|_ BCL|BCL|NNP|_ base|base|NN|_ call|call|NN|_ files|file|NNS|_ as|as|IN|_ primary|primary|JJ|_ sequencing|sequencing|NN|_ output|output|NN|_ in|in|IN|_ bcl2|bcl2|NN|_ format|format|NN|_ .|.|.|_ Conversion|conversion|NN|_ of|of|IN|_ the|the|DT|_ bcl2|bcl2|NN|_ file|file|NN|_ to|to|TO|_ gzipped|gzipped|JJ|_ fastq|fastq|NN|_ files|file|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ bcl2fastq|bcl2fastq|NN|_ script|script|NN|_ v.|v.|CC|_ 2.18.0.12|2.18.0.12|CD|_ provided|provide|VBN|_ by|by|IN|_ Illumina|Illumina|NNP|_ .|.|.|_
Quality|Quality|NNP|_ and|and|CC|_ adapter|adapter|NN|_ trimming|trim|VBG|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ software|software|NN|_ package|package|NN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Trim|trim|VBP|_ Sequences|sequence|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
Mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ was|be|VBD|_ also|also|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Map|map|NN|_ Reads|read|VBZ|_ to|to|TO|_ Reference|Reference|NNP|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
For|for|IN|_ quantification|quantification|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ read|read|NN|_ counting|counting|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ alignments|alignment|NNS|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ Genomics|Genomics|NNP|_ Workbench|Workbench|NNP|_ were|be|VBD|_ exported|export|VBN|_ in|in|IN|_ BAM|BAM|NNP|_ format|format|NN|_ .|.|.|_ Read|Read|NNP|_ counting|counting|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ FeatureCounts|FeatureCounts|NNP|_ v.|v.|CC|_ 1.5.0-p1|1.5.0-p1|CD|_ program|program|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ Level|Level|NNP|_ :|:|:|_ meta-feature|meta-feature|JJ|_ leve|leve|NN|_ .|.|.|_ Paired-end|paired-end|NN|_ :|:|:|_ no|no|DT|_ .|.|.|_ Strand|strand|VB|_ specific|specific|JJ|_ :|:|:|_ yes|yes|UH|_ .|.|.|_ Multimapping|multimapp|VBG|_ reads|read|VBZ|_ :|:|:|_ counted|count|VBN|_ -LRB-|-lrb-|-LRB-|_ as|as|IN|_ fractions|fraction|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Multi-overlapping|multi-overlapping|JJ|_ reads|read|VBZ|_ :|:|:|_ not|not|RB|_ counted|count|VBN|_ .|.|.|_ Overlapping|overlapping|JJ|_ bases|basis|NNS|_ :|:|:|_ 30|30|CD|_ .|.|.|_ Read|Read|NNP|_ orientations|orientation|NNS|_ :|:|:|_ fr|fr|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 017626.1|017626.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Strain-expression|strain-expression|NN|_ .|.|.|_ xlsx|xlsx|NN|_ archive|archive|NN|_ contains|contain|VBZ|_ expression|expression|NN|_ values|value|NNS|_ in|in|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Reads|read|NNS|_ Per|per|IN|_ Kb|kb|NN|_ exon|exon|NN|_ -LRB-|-lrb-|-LRB-|_ contig|contig|NN|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ Million|Million|NNP|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ Mortazavi|Mortazavi|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ .|.|.|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 621-8|621-8|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ can|can|MD|GEN be|be|VB|_ directly|directly|RB|_ compared|compare|VBN|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ -RRB-|-rrb-|-RRB-|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ mill|mill|NN|_ and|and|CC|_ the|the|DT|_ mirVana|mirvana|NN|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ including|include|VBG|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
From|from|IN|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ first-strand|first-strand|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ After|after|IN|_ fragmentation|fragmentation|NN|_ ,|,|,|_ the|the|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ in|in|IN|_ a|a|DT|_ strand|strand|NN|_ specific|specific|JJ|_ manner|manner|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ For|for|IN|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ ,|,|,|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ a|a|DT|_ 25:1|25:1|CD|_ ratio|ratio|NN|_ .|.|.|_ The|the|DT|_ library|library|NN|_ pool|pool|NN|_ was|be|VBD|_ fractionated|fractionate|VBN|_ in|in|IN|_ the|the|DT|_ size|size|NN|_ range|range|NN|_ of|of|IN|_ 250-500|250-500|CD|_ bp|bp|NN|_ using|use|VBG|_ a|a|DT|_ differential|differential|JJ|_ clean|clean|JJ|_ -|-|:|_ up|up|RP|_ with|with|IN|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ kit|kit|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ pool|pool|NN|_ was|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ using|use|VBG|_ 75|75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_
LB|LB|NNP|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
cell|cell|NN|_ pellets|pellet|NNS|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ mutant|mutant|JJ|_ hnshns2|hnshns2|NN|_
LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
cell|cell|NN|_ pellets|pellet|NNS|_
Mario|Mario|NNP|_ ,|,|,|_ ,|,|,|_ Huttener|Huttener|NNP|_ Queiroz|Queiroz|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PLYS|plys|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ M1|m1|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PSB1C3|psb1c3|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PD864|pd864|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ LACZ|lacz|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ rhamnose|rhamnose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PLYS|plys|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PLYS|plys|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ M1|m1|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PSB1C3|psb1c3|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ Lux|lux|FW|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PSB1C3|psb1c3|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ Lux|lux|FW|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PD864|pd864|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ LACZ|lacz|NN|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ rhamnose|rhamnose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PSB1C3|psb1c3|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PLYS|plys|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PD864|pd864|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ rhamnose|rhamnose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PLYS|plys|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ M1|m1|NN|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PSB1C3|psb1c3|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PSB1C3|psb1c3|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PSB1C3|psb1c3|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ H3|h3|NN|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PSB1C3|psb1c3|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ Lux|lux|FW|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PSB1C3|psb1c3|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ Lux|lux|FW|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PD864|pd864|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ LACZ|lacz|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ rhamnose|rhamnose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PD864|pd864|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ rhamnose|rhamnose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PLYS|plys|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ M1|m1|NN|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PD864|pd864|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ rhamnose|rhamnose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
Simone|Simone|NNP|_ ,|,|,|_ ,|,|,|_ Furini|Furini|NNP|_
3C-seq|3c-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ proccessed|proccess|VBN|_ using|use|VBG|_ the|the|DT|_ 3C-seq|3c-seq|JJ|_ pipeline|pipeline|NN|_ available|available|JJ|_ at|at|IN|_ -LRB-|-lrb-|-LRB-|_ https://github.com/koszullab/|https://github.com/koszullab/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Removal|removal|NN|_ of|of|IN|_ PCR|pcr|NN|_ duplicates|duplicate|VBZ|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ 20|20|CD|_ first|first|JJ|_ bp|bp|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ containing|contain|VBG|_ a|a|DT|_ 6|6|CD|_ nt|nt|NN|_ random|random|JJ|_ tag|tag|NN|GEN -LRB-|-lrb-|-LRB-|_ home|home|NN|_ made|make|VBN|_ script|script|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Iterative|iterative|JJ|_ alignment|alignment|NN|_ ,|,|,|_ Min-leght|min-leght|NN|_ =|=|JJ|_ 20|20|CD|_ ,|,|,|_ step|step|NN|_ =|=|JJ|_ 5|5|CD|_ ,|,|,|_ bowtie2|bowtie2|NN|_ --|--|:|_ very-sensitive|very-sensitive|JJ|_
Filtering|filter|VBG|_ ,|,|,|_ Mapping|mapping|NN|_ quality|quality|NN|_ =|=|JJ|_ 30|30|CD|_ ,|,|,|_ no|no|DT|_ ambiguous|ambiguous|JJ|_ reads|read|VBZ|_
Assignment|Assignment|NNP|_ to|to|TO|_ restriction|restriction|NN|_ fragment|fragment|NN|_
Removal|removal|NN|_ of|of|IN|_ un-informative|un-informative|JJ|_ events|event|NNS|_ -LRB-|-lrb-|-LRB-|_ uncuts|uncut|NNS|_ ,|,|,|_ loops|loop|NNS|_ etc|etc|FW|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Cournac|Cournac|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ BMC|BMC|NNP|_ 2012|2012|CD|_ .|.|.|_
Binning|binning|NN|_ at|at|IN|_ 5kb|5kb|JJ|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_ ,|,|,|_ total|total|JJ|_ length|length|NN|_ :|:|:|_ 4639675|4639675|CD|_ bp|bp|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ rna-seq|rna-seq|NN|_ :|:|:|_ genomic|genomic|JJ|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ middle|middle|NN|_ of|of|IN|_ the|the|DT|_ 5kb-bin|5kb-bin|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ each|each|DT|_ count|count|NN|_ .|.|.|_ 3C|3c|NN|_ seq|seq|NN|_ :|:|:|_ contact|contact|NN|_ maps|map|NNS|_ -LRB-|-lrb-|-LRB-|_ 2D|2d|NN|_ array|array|NN|_ of|of|IN|_ 928|928|CD|_ 5kb-bins|5kb-bin|NNS|_ x|x|CC|_ 928|928|CD|_ 5kb-bins|5kb-bin|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Protect|protect|VB|_ Bacteria|bacterium|NNS|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -|-|:|_ #|#|#|_ 74524|74524|CD|_ -RRB-|-rrb-|-RRB-|_
For|for|IN|_ 3C-seq|3c-seq|NN|_ :|:|:|_ ≈|≈|SYM|_ 1-2|1-2|CD|_ x|x|CC|_ 109|109|CD|_ crosslinked|crosslink|VBN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ -RRB-|-rrb-|-RRB-|_ are|be|VBP|_ suspended|suspend|VBN|_ in|in|IN|_ 600|600|CD|_ μl|μl|NN|_ Tris|Tris|NNP|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -LRB-|-lrb-|-LRB-|_ TE|te|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 4|4|CD|_ μl|μl|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ 35|35|CD|_ U/μl|u/μl|NN|_ ;|;|:|_ Tebu|Tebu|NNP|_ Bio|Bio|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ RT|rt|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ .|.|.|_ SDS|sds|NN|_ is|be|VBZ|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ mix|mix|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ 0.5|0.5|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ are|be|VBP|_ incubated|incubate|VBN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT.|RT.|NNP|_ 50μl|50μl|CD|_ of|of|IN|_ lysed|lysed|JJ|_ cells|cell|NNS|_ are|be|VBP|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ tubes|tube|NNS|_ containing|contain|VBG|_ 450μL|450μl|NN|_ of|of|IN|_ digestion|digestion|NN|_ mix|mix|NN|_ -LRB-|-lrb-|-LRB-|_ 1X|1x|NN|_ NEB|neb|NN|_ 1|1|CD|_ buffer|buffer|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ triton|triton|NN|_ X-100|x-100|NN|_ ,|,|,|_ and|and|CC|_ 100U|100u|NN|_ HpaII|hpaii|NN|_ enzyme|enzyme|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ is|be|VBZ|_ digested|digest|VBN|_ for|for|IN|_ 3|3|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ split|split|NN|_ in|in|IN|_ 4|4|CD|_ aliquots|aliquot|NNS|_ ,|,|,|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ 8|8|CD|_ ml|ml|NN|_ ligation|ligation|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 1X|1x|NN|_ ligation|ligation|NN|_ buffer|buffer|NN|_ NEB|neb|NN|_ without|without|IN|_ ATP|atp|NN|SUPP ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ATP|atp|NN|SUPP ,|,|,|_ 0.1|0.1|CD|_ mg/ml|mg/ml|JJ|_ BSA|bsa|NN|_ ,|,|,|_ 125|125|CD|_ Units|unit|NNS|_ of|of|IN|_ T4|t4|NN|_ DNA|dna|NN|_ ligase|ligase|NN|_ 5|5|CD|_ U/μl|u/μl|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ligation|ligation|NN|_ is|be|VBZ|_ then|then|RB|_ performed|perform|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ incubation|incubation|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ON|on|IN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ in|in|IN|_ presence|presence|NN|_ of|of|IN|_ 250|250|CD|_ μg/ml|μg/ml|JJ|_ proteinase|proteinase|NN|_ K|k|NN|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ .|.|.|_ Precipitation|precipitation|NN|_ of|of|IN|_ DNA|dna|NN|_ is|be|VBZ|_ performed|perform|VBN|_ using|use|VBG|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ 3|3|CD|_ M|m|NN|_ Na-Acetate|na-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ two|two|CD|_ volumes|volume|NNS|_ of|of|IN|_ iso-propanol|iso-propanol|NN|_ .|.|.|_ After|after|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ ,|,|,|_ DNA|dna|NN|_ is|be|VBZ|_ pelleted|pelleted|JJ|_ ,|,|,|_ suspended|suspend|VBN|_ in|in|IN|_ 500μl|500μl|JJ|_ 1X|1x|NN|_ TE|te|NN|_ buffer|buffer|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ presence|presence|NN|_ of|of|IN|_ RNAse|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 0.03|0.03|CD|_ mg/ml|mg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ is|be|VBZ|_ then|then|RB|_ transferred|transfer|VBN|_ into|into|IN|_ 2|2|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tubes|tube|NNS|_ ,|,|,|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 500|500|CD|_ μl|μl|NN|_ phenol-chloroform|phenol-chloroform|NN|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ precipitated|precipitated|JJ|_ ,|,|,|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ cold|cold|JJ|_ ethanol|ethanol|NN|_ 70|70|CD|_ %|%|NN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ 30|30|CD|_ μl|μl|NN|_ 1X|1x|NN|_ TE|te|NN|_ buffer|buffer|NN|_ .|.|.|_ All|all|DT|_ tubes|tube|NNS|_ are|be|VBP|_ pooled|pool|VBN|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ 3C|3c|NN|_ library|library|NN|_ is|be|VBZ|_ quantified|quantify|VBN|_ on|on|IN|_ gel|gel|NN|_ using|use|VBG|_ Quantity|Quantity|NNP|_ One|one|CD|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ BioRad|biorad|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
3C-seq|3c-seq|NN|_ :|:|:|_ 5|5|CD|_ µg|µg|NN|_ of|of|IN|_ a|a|DT|_ 3C|3c|NN|_ library|library|NN|_ was|be|VBD|_ suspended|suspend|VBN|_ in|in|IN|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ volume|volume|NN|_ 130|130|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sheared|shear|VBD|_ using|use|VBG|_ a|a|DT|_ Covaris|Covaris|NNP|_ S220|s220|NN|_ instrument|instrument|NN|_ -LRB-|-lrb-|-LRB-|_ Duty|duty|NN|_ cycle|cycle|NN|_ 5|5|CD|_ ,|,|,|_ Intensity|intensity|NN|_ 5|5|CD|_ ,|,|,|_ cycles/burst|cycles/burst|NN|_ 200|200|CD|_ ,|,|,|_ time|time|NN|_ 60|60|CD|_ sec|sec|NN|_ for|for|IN|_ 4|4|CD|_ cycles|cycle|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ Paired-End|paired-end|NN|_ DNA|dna|NN|_ sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ --|--|:|_ Illumina|Illumina|NNP|_ --|--|:|_ PE-930-1001|pe-930-1001|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ DNA|dna|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ custom-made|custom-made|JJ|_ adapters|adapter|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ Marbouty|Marbouty|NNP|_ M.|M.|NNP|_ et|et|NNP|_ al|al|NNP|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Mol|Mol|NNP|_ Cell|cell|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ Tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ ranging|range|VBG|_ in|in|IN|_ size|size|NN|_ from|from|IN|_ 400|400|CD|_ to|to|TO|_ 900|900|CD|_ pb|pb|NN|_ were|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ a|a|DT|_ PippinPrep|PippinPrep|NNP|_ apparatus|apparatus|NN|_ -LRB-|-lrb-|-LRB-|_ SAGE|sage|NN|_ Science|science|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ each|each|DT|_ library|library|NN|_ ,|,|,|_ four|four|CD|_ test|test|NN|_ PCR|pcr|NN|_ reactions|reaction|NNS|_ were|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ determine|determine|VB|_ the|the|DT|_ optimal|optimal|JJ|_ number|number|NN|_ of|of|IN|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ or|or|CC|_ 2|2|CD|_ µL|µl|NN|_ of|of|IN|_ the|the|DT|_ collected|collect|VBN|_ DNA|dna|NN|_ ,|,|,|_ Illumina|Illumina|NNP|_ primers|primer|NNS|_ PE1|pe1|NN|_ .0|.0|NN|_ and|and|CC|_ PE2|pe2|NN|_ .0|.0|CD|_ using|use|VBG|_ Taq|taq|NN|_ Phusion|phusion|NN|_ -LSB-|-lsb-|-LRB-|_ Finnzymes|finnzyme|NNS|_ -RSB-|-rsb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ large-scale|large-scale|JJ|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 8|8|CD|_ reactions|reaction|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ then|then|RB|_ set-up|set-up|JJ|_ with|with|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ determined|determine|VBN|_ previously|previously|RB|_ .|.|.|_ The|the|DT|_ PCR|pcr|NN|_ product|product|NN|_ was|be|VBD|_ finally|finally|RB|_ purified|purify|VBN|_ on|on|IN|_ Qiagen|Qiagen|NNP|_ MinElute|MinElute|NNP|_ columns|column|NNS|_ and|and|CC|_ subject|subject|JJ|_ to|to|TO|_ paired-end|paired-end|NN|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ sequencer|sequencer|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 22|22|CD|_ °C|°c|NN|_ ,|,|,|_ 30|30|CD|_ °C|°c|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ either|either|CC|_ Lennox|Lennox|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ liquid|liquid|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ A|a|DT|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.12|0.12|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ -LRB-|-lrb-|-LRB-|_ early|early|JJ|_ exponential|exponential|JJ|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E|e|NN|_ coli|coli|NN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ MM|mm|NN|_ +|+|CC|_ 0.12|0.12|CD|_ %|%|NN|_ casaminoacids|casaminoacid|NNS|_ +0.4|+0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ 30|30|CD|_ °C|°c|NN|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 22|22|CD|_ °C|°c|NN|_ ,|,|,|_ 30|30|CD|_ °C|°c|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ either|either|CC|_ Lennox|Lennox|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ liquid|liquid|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ A|a|DT|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.12|0.12|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ -LRB-|-lrb-|-LRB-|_ early|early|JJ|_ exponential|exponential|JJ|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E|e|NN|_ coli|coli|NN|_ cells|cell|NNS|_
Axel|Axel|NNP|_ ,|,|,|_ ,|,|,|_ Cournac|Cournac|NNP|_
3C-seq|3c-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ proccessed|proccess|VBN|_ using|use|VBG|_ the|the|DT|_ 3C-seq|3c-seq|JJ|_ pipeline|pipeline|NN|_ available|available|JJ|_ at|at|IN|_ -LRB-|-lrb-|-LRB-|_ https://github.com/koszullab/|https://github.com/koszullab/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Removal|removal|NN|_ of|of|IN|_ PCR|pcr|NN|_ duplicates|duplicate|VBZ|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ 20|20|CD|_ first|first|JJ|_ bp|bp|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ containing|contain|VBG|_ a|a|DT|_ 6|6|CD|_ nt|nt|NN|_ random|random|JJ|_ tag|tag|NN|GEN -LRB-|-lrb-|-LRB-|_ home|home|NN|_ made|make|VBN|_ script|script|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Iterative|iterative|JJ|_ alignment|alignment|NN|_ ,|,|,|_ Min-leght|min-leght|NN|_ =|=|JJ|_ 20|20|CD|_ ,|,|,|_ step|step|NN|_ =|=|JJ|_ 5|5|CD|_ ,|,|,|_ bowtie2|bowtie2|NN|_ --|--|:|_ very-sensitive|very-sensitive|JJ|_
Filtering|filter|VBG|_ ,|,|,|_ Mapping|mapping|NN|_ quality|quality|NN|_ =|=|JJ|_ 30|30|CD|_ ,|,|,|_ no|no|DT|_ ambiguous|ambiguous|JJ|_ reads|read|VBZ|_
Assignment|Assignment|NNP|_ to|to|TO|_ restriction|restriction|NN|_ fragment|fragment|NN|_
Removal|removal|NN|_ of|of|IN|_ un-informative|un-informative|JJ|_ events|event|NNS|_ -LRB-|-lrb-|-LRB-|_ uncuts|uncut|NNS|_ ,|,|,|_ loops|loop|NNS|_ etc|etc|FW|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Cournac|Cournac|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ BMC|BMC|NNP|_ 2012|2012|CD|_ .|.|.|_
Binning|binning|NN|_ at|at|IN|_ 5kb|5kb|JJ|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_ ,|,|,|_ total|total|JJ|_ length|length|NN|_ :|:|:|_ 4639675|4639675|CD|_ bp|bp|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ rna-seq|rna-seq|NN|_ :|:|:|_ genomic|genomic|JJ|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ middle|middle|NN|_ of|of|IN|_ the|the|DT|_ 5kb-bin|5kb-bin|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ each|each|DT|_ count|count|NN|_ .|.|.|_ 3C|3c|NN|_ seq|seq|NN|_ :|:|:|_ contact|contact|NN|_ maps|map|NNS|_ -LRB-|-lrb-|-LRB-|_ 2D|2d|NN|_ array|array|NN|_ of|of|IN|_ 928|928|CD|_ 5kb-bins|5kb-bin|NNS|_ x|x|CC|_ 928|928|CD|_ 5kb-bins|5kb-bin|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
For|for|IN|_ 3C-seq|3c-seq|NN|_ :|:|:|_ ≈|≈|SYM|_ 1-2|1-2|CD|_ x|x|CC|_ 109|109|CD|_ crosslinked|crosslink|VBN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ -RRB-|-rrb-|-RRB-|_ are|be|VBP|_ suspended|suspend|VBN|_ in|in|IN|_ 600|600|CD|_ μl|μl|NN|_ Tris|Tris|NNP|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -LRB-|-lrb-|-LRB-|_ TE|te|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 4|4|CD|_ μl|μl|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ 35|35|CD|_ U/μl|u/μl|NN|_ ;|;|:|_ Tebu|Tebu|NNP|_ Bio|Bio|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ RT|rt|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ .|.|.|_ SDS|sds|NN|_ is|be|VBZ|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ mix|mix|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ 0.5|0.5|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ are|be|VBP|_ incubated|incubate|VBN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT.|RT.|NNP|_ 50μl|50μl|CD|_ of|of|IN|_ lysed|lysed|JJ|_ cells|cell|NNS|_ are|be|VBP|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ tubes|tube|NNS|_ containing|contain|VBG|_ 450μL|450μl|NN|_ of|of|IN|_ digestion|digestion|NN|_ mix|mix|NN|_ -LRB-|-lrb-|-LRB-|_ 1X|1x|NN|_ NEB|neb|NN|_ 1|1|CD|_ buffer|buffer|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ triton|triton|NN|_ X-100|x-100|NN|_ ,|,|,|_ and|and|CC|_ 100U|100u|NN|_ HpaII|hpaii|NN|_ enzyme|enzyme|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ is|be|VBZ|_ digested|digest|VBN|_ for|for|IN|_ 3|3|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ split|split|NN|_ in|in|IN|_ 4|4|CD|_ aliquots|aliquot|NNS|_ ,|,|,|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ 8|8|CD|_ ml|ml|NN|_ ligation|ligation|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 1X|1x|NN|_ ligation|ligation|NN|_ buffer|buffer|NN|_ NEB|neb|NN|_ without|without|IN|_ ATP|atp|NN|SUPP ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ATP|atp|NN|SUPP ,|,|,|_ 0.1|0.1|CD|_ mg/ml|mg/ml|JJ|_ BSA|bsa|NN|_ ,|,|,|_ 125|125|CD|_ Units|unit|NNS|_ of|of|IN|_ T4|t4|NN|_ DNA|dna|NN|_ ligase|ligase|NN|_ 5|5|CD|_ U/μl|u/μl|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ligation|ligation|NN|_ is|be|VBZ|_ then|then|RB|_ performed|perform|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ incubation|incubation|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ON|on|IN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ in|in|IN|_ presence|presence|NN|_ of|of|IN|_ 250|250|CD|_ μg/ml|μg/ml|JJ|_ proteinase|proteinase|NN|_ K|k|NN|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ .|.|.|_ Precipitation|precipitation|NN|_ of|of|IN|_ DNA|dna|NN|_ is|be|VBZ|_ performed|perform|VBN|_ using|use|VBG|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ 3|3|CD|_ M|m|NN|_ Na-Acetate|na-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ two|two|CD|_ volumes|volume|NNS|_ of|of|IN|_ iso-propanol|iso-propanol|NN|_ .|.|.|_ After|after|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ ,|,|,|_ DNA|dna|NN|_ is|be|VBZ|_ pelleted|pelleted|JJ|_ ,|,|,|_ suspended|suspend|VBN|_ in|in|IN|_ 500μl|500μl|JJ|_ 1X|1x|NN|_ TE|te|NN|_ buffer|buffer|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ presence|presence|NN|_ of|of|IN|_ RNAse|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 0.03|0.03|CD|_ mg/ml|mg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ is|be|VBZ|_ then|then|RB|_ transferred|transfer|VBN|_ into|into|IN|_ 2|2|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tubes|tube|NNS|_ ,|,|,|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 500|500|CD|_ μl|μl|NN|_ phenol-chloroform|phenol-chloroform|NN|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ precipitated|precipitated|JJ|_ ,|,|,|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ cold|cold|JJ|_ ethanol|ethanol|NN|_ 70|70|CD|_ %|%|NN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ 30|30|CD|_ μl|μl|NN|_ 1X|1x|NN|_ TE|te|NN|_ buffer|buffer|NN|_ .|.|.|_ All|all|DT|_ tubes|tube|NNS|_ are|be|VBP|_ pooled|pool|VBN|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ 3C|3c|NN|_ library|library|NN|_ is|be|VBZ|_ quantified|quantify|VBN|_ on|on|IN|_ gel|gel|NN|_ using|use|VBG|_ Quantity|Quantity|NNP|_ One|one|CD|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ BioRad|biorad|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
3C-seq|3c-seq|NN|_ :|:|:|_ 5|5|CD|_ µg|µg|NN|_ of|of|IN|_ a|a|DT|_ 3C|3c|NN|_ library|library|NN|_ was|be|VBD|_ suspended|suspend|VBN|_ in|in|IN|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ volume|volume|NN|_ 130|130|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sheared|shear|VBD|_ using|use|VBG|_ a|a|DT|_ Covaris|Covaris|NNP|_ S220|s220|NN|_ instrument|instrument|NN|_ -LRB-|-lrb-|-LRB-|_ Duty|duty|NN|_ cycle|cycle|NN|_ 5|5|CD|_ ,|,|,|_ Intensity|intensity|NN|_ 5|5|CD|_ ,|,|,|_ cycles/burst|cycles/burst|NN|_ 200|200|CD|_ ,|,|,|_ time|time|NN|_ 60|60|CD|_ sec|sec|NN|_ for|for|IN|_ 4|4|CD|_ cycles|cycle|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ Paired-End|paired-end|NN|_ DNA|dna|NN|_ sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ --|--|:|_ Illumina|Illumina|NNP|_ --|--|:|_ PE-930-1001|pe-930-1001|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ DNA|dna|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ custom-made|custom-made|JJ|_ adapters|adapter|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ Marbouty|Marbouty|NNP|_ M.|M.|NNP|_ et|et|NNP|_ al|al|NNP|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Mol|Mol|NNP|_ Cell|cell|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ Tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ ranging|range|VBG|_ in|in|IN|_ size|size|NN|_ from|from|IN|_ 400|400|CD|_ to|to|TO|_ 900|900|CD|_ pb|pb|NN|_ were|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ a|a|DT|_ PippinPrep|PippinPrep|NNP|_ apparatus|apparatus|NN|_ -LRB-|-lrb-|-LRB-|_ SAGE|sage|NN|_ Science|science|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ each|each|DT|_ library|library|NN|_ ,|,|,|_ four|four|CD|_ test|test|NN|_ PCR|pcr|NN|_ reactions|reaction|NNS|_ were|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ determine|determine|VB|_ the|the|DT|_ optimal|optimal|JJ|_ number|number|NN|_ of|of|IN|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ or|or|CC|_ 2|2|CD|_ µL|µl|NN|_ of|of|IN|_ the|the|DT|_ collected|collect|VBN|_ DNA|dna|NN|_ ,|,|,|_ Illumina|Illumina|NNP|_ primers|primer|NNS|_ PE1|pe1|NN|_ .0|.0|NN|_ and|and|CC|_ PE2|pe2|NN|_ .0|.0|CD|_ using|use|VBG|_ Taq|taq|NN|_ Phusion|phusion|NN|_ -LSB-|-lsb-|-LRB-|_ Finnzymes|finnzyme|NNS|_ -RSB-|-rsb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ large-scale|large-scale|JJ|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 8|8|CD|_ reactions|reaction|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ then|then|RB|_ set-up|set-up|JJ|_ with|with|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ determined|determine|VBN|_ previously|previously|RB|_ .|.|.|_ The|the|DT|_ PCR|pcr|NN|_ product|product|NN|_ was|be|VBD|_ finally|finally|RB|_ purified|purify|VBN|_ on|on|IN|_ Qiagen|Qiagen|NNP|_ MinElute|MinElute|NNP|_ columns|column|NNS|_ and|and|CC|_ subject|subject|JJ|_ to|to|TO|_ paired-end|paired-end|NN|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ sequencer|sequencer|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 22|22|CD|_ °C|°c|NN|_ ,|,|,|_ 30|30|CD|_ °C|°c|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ either|either|CC|_ Lennox|Lennox|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ liquid|liquid|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ A|a|DT|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.12|0.12|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ -LRB-|-lrb-|-LRB-|_ early|early|JJ|_ exponential|exponential|JJ|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E|e|NN|_ coli|coli|NN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ MM|mm|NN|_ +|+|CC|_ 0.12|0.12|CD|_ %|%|NN|_ casaminoacids|casaminoacid|NNS|_ +0.4|+0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ 30|30|CD|_ °C|°c|NN|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 22|22|CD|_ °C|°c|NN|_ ,|,|,|_ 30|30|CD|_ °C|°c|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ either|either|CC|_ Lennox|Lennox|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ liquid|liquid|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ A|a|DT|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.12|0.12|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ -LRB-|-lrb-|-LRB-|_ early|early|JJ|_ exponential|exponential|JJ|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E|e|NN|_ coli|coli|NN|_ cells|cell|NNS|_
Axel|Axel|NNP|_ ,|,|,|_ ,|,|,|_ Cournac|Cournac|NNP|_
Paired-end|paired-end|NN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_ Any|any|DT|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ removed|remove|VBN|_ prior|prior|RB|_ to|to|TO|_ mapping|mapping|NN|_ .|.|.|_
For|for|IN|_ each|each|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ all|all|DT|_ mapped|map|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ at|at|IN|_ all|all|DT|_ aligned|align|VBN|_ positions|position|NNS|_ a|a|DT|_ count|count|NN|_ was|be|VBD|_ added|add|VBN|_ .|.|.|_
Counts|Counts|NNPS|_ were|be|VBD|_ depth|depth|NN|_ normalized|normalize|VBD|_ to|to|TO|_ a|a|DT|_ pseudo-reference|pseudo-reference|NN|_ sample|sample|NN|_ calculated|calculate|VBN|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ using|use|VBG|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ counts|count|NNS|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
For|for|IN|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ ,|,|,|_ counts|count|VBZ|_ at|at|IN|_ all|all|DT|_ positions|position|NNS|_ were|be|VBD|_ log2|log2|NN|_ transformed|transform|VBN|_ and|and|CC|_ a|a|DT|_ cleavage|cleavage|NN|_ ratio|ratio|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ MazF|mazf|NN|_ -|-|:|_ empty|empty|JJ|_ vector|vector|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ assessing|assess|VBG|_ MazF|mazf|NN|_ cleavage|cleavage|NN|_ in|in|IN|_ transcripts|transcript|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ 5m_ribozero_counts_cleavage_ratio.csv.gz|5m_ribozero_counts_cleavage_ratio.csv.gz|NN|_ is|be|VBZ|_ a|a|DT|_ log-transformed|log-transformed|JJ|_ list|list|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ depth-normalized|depth-normalized|JJ|_ counts|count|NNS|_ for|for|IN|_ every|every|DT|_ genomic|genomic|JJ|_ position|position|NN|_ at|at|IN|_ both|both|DT|_ strands|strand|NNS|_ for|for|IN|_ each|each|DT|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ sample|sample|NN|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ average|average|JJ|_ cleavage|cleavage|NN|_ ratio|ratio|NN|_ calculated|calculate|VBN|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_ total_RNA_rpm.csv.gz|total_rna_rpm.csv.gz|NN|_ is|be|VBZ|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ depth-normalized|depth-normalized|JJ|_ counts|count|NNS|_ for|for|IN|_ every|every|DT|_ genomic|genomic|JJ|_ position|position|NN|_ at|at|IN|_ both|both|DT|_ strans|stran|NNS|_ for|for|IN|_ all|all|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Direct-zol|direct-zol|NN|_ RNA|rna|NN|_ MiniPrep|MiniPrep|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|zymo|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
See|see|VB|_ publication|publication|NN|_ for|for|IN|_ complete|complete|JJ|_ protocol|protocol|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ samples|sample|NNS|_ with|with|IN|_ rRNA|rrna|NN|_ subtraction|subtraction|NN|_ with|with|IN|_ treated|treat|VBN|_ with|with|IN|_ bacterial|bacterial|JJ|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ with|with|IN|_ RNA|rna|NN|_ fragmentation|fragmentation|NN|_ reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ First|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ random|random|JJ|_ primers|primer|NNS|_ and|and|CC|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ enable|enable|VB|_ strand|strand|NN|_ specificity|specificity|NN|_ ,|,|,|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ dUTP|dutp|NN|_ instead|instead|RB|_ of|of|IN|_ dTTP|dttp|NN|_ with|with|IN|_ RNase|rnase|NN|_ H|h|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ ligase|ligase|NN|_ ,|,|,|_ and|and|CC|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ Ends|end|NNS|_ were|be|VBD|_ repaired|repair|VBN|_ with|with|IN|_ T4|t4|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ ,|,|,|_ Klenow|Klenow|NNP|_ DNA|DNA|NNP|_ polymerase|polymerase|NN|_ ,|,|,|_ and|and|CC|_ T4|t4|NN|_ PNK|pnk|NN|_ .|.|.|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ the|the|DT|_ Klenow|Klenow|NNP|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ '|'|''|_ >|>|JJR|_ 5|5|CD|_ '|'|''|_ exo|exo|SYM|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Y-shaped|y-shaped|JJ|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ and|and|CC|_ 9-12|9-12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ primers|primer|NNS|_ with|with|IN|_ multiplexing|multiplex|VBG|_ indexes|index|NNS|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ an|a|DT|_ acrylamide|acrylamide|NN|_ gel|gel|NN|_ and|and|CC|_ submitted|submit|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ at|at|IN|_ the|the|DT|_ MIT|MIT|NNP|_ BioMicro|BioMicro|NNP|_ Center|Center|NNP|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
Separate|separate|JJ|_ E.|e.|FW|_ coli|coli|FW|_ colonies|colony|NNS|_ were|be|VBD|_ picked|pick|VBN|_ from|from|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ for|for|IN|_ each|each|DT|_ replicate|replicate|VBP|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 12-16|12-16|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ and|and|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ fresh|fresh|JJ|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ 3-4|3-4|CD|_ hours|hour|NNS|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.35|0.35|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaker|shaker|NN|_ at|at|IN|_ 200|200|CD|_ RPM|rpm|NN|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ washed|wash|VBN|_ ,|,|,|_ and|and|CC|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ media|media|NNS|_ lacking|lack|VBG|_ glucose|glucose|NN|SUPP .|.|.|_ After|after|IN|_ at|at|IN|_ least|least|JJS|_ 30|30|CD|_ minutes|minute|NNS|_ of|of|IN|_ recovery|recovery|NN|_ Para|para|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ adding|add|VBG|_ arabinose|arabinose|NN|_ to|to|TO|_ 0.2|0.2|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ for|for|IN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ on|on|IN|_ a|a|DT|_ benchtop|benchtop|JJ|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ flash|flash|VB|_ frozen|freeze|VBN|_ in|in|IN|_ lN2|ln2|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ delta|delta|NN|_ _|_|CD|_ mazF|mazf|NN|GEN
plasmid|plasmid|NN|_ :|:|:|_ pBAD30-empty|pbad30-empty|NN|_
ribozero|ribozero|NN|_ :|:|:|_ Yes|yes|UH|_
ercc|ercc|JJ|_ spike-in|spike-in|NN|_ :|:|:|_ No|no|DT|_
time|time|NN|_ induction|induction|NN|_ :|:|:|_ 5|5|CD|_ minutes|minute|NNS|_
Separate|separate|JJ|_ E.|e.|FW|_ coli|coli|FW|_ colonies|colony|NNS|_ were|be|VBD|_ picked|pick|VBN|_ from|from|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ for|for|IN|_ each|each|DT|_ replicate|replicate|VBP|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 12-16|12-16|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ and|and|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ fresh|fresh|JJ|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ 3-4|3-4|CD|_ hours|hour|NNS|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.35|0.35|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaker|shaker|NN|_ at|at|IN|_ 200|200|CD|_ RPM|rpm|NN|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ washed|wash|VBN|_ ,|,|,|_ and|and|CC|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ media|media|NNS|_ lacking|lack|VBG|_ glucose|glucose|NN|SUPP .|.|.|_ After|after|IN|_ at|at|IN|_ least|least|JJS|_ 30|30|CD|_ minutes|minute|NNS|_ of|of|IN|_ recovery|recovery|NN|_ Para|para|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ adding|add|VBG|_ arabinose|arabinose|NN|_ to|to|TO|_ 0.2|0.2|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ for|for|IN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ on|on|IN|_ a|a|DT|_ benchtop|benchtop|JJ|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ flash|flash|VB|_ frozen|freeze|VBN|_ in|in|IN|_ lN2|ln2|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_
Peter|Peter|NNP|_ ,|,|,|_ ,|,|,|_ Culviner|Culviner|NNP|_
Paired-end|paired-end|NN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_ Any|any|DT|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ removed|remove|VBN|_ prior|prior|RB|_ to|to|TO|_ mapping|mapping|NN|_ .|.|.|_
For|for|IN|_ each|each|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ all|all|DT|_ mapped|map|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ at|at|IN|_ all|all|DT|_ aligned|align|VBN|_ positions|position|NNS|_ a|a|DT|_ count|count|NN|_ was|be|VBD|_ added|add|VBN|_ .|.|.|_
Counts|Counts|NNPS|_ were|be|VBD|_ depth|depth|NN|_ normalized|normalize|VBD|_ to|to|TO|_ a|a|DT|_ pseudo-reference|pseudo-reference|NN|_ sample|sample|NN|_ calculated|calculate|VBN|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ using|use|VBG|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ counts|count|NNS|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
For|for|IN|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ ,|,|,|_ counts|count|VBZ|_ at|at|IN|_ all|all|DT|_ positions|position|NNS|_ were|be|VBD|_ log2|log2|NN|_ transformed|transform|VBN|_ and|and|CC|_ a|a|DT|_ cleavage|cleavage|NN|_ ratio|ratio|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ MazF|mazf|NN|_ -|-|:|_ empty|empty|JJ|_ vector|vector|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ assessing|assess|VBG|_ MazF|mazf|NN|_ cleavage|cleavage|NN|_ in|in|IN|_ transcripts|transcript|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ 5m_ribozero_counts_cleavage_ratio.csv.gz|5m_ribozero_counts_cleavage_ratio.csv.gz|NN|_ is|be|VBZ|_ a|a|DT|_ log-transformed|log-transformed|JJ|_ list|list|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ depth-normalized|depth-normalized|JJ|_ counts|count|NNS|_ for|for|IN|_ every|every|DT|_ genomic|genomic|JJ|_ position|position|NN|_ at|at|IN|_ both|both|DT|_ strands|strand|NNS|_ for|for|IN|_ each|each|DT|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ sample|sample|NN|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ average|average|JJ|_ cleavage|cleavage|NN|_ ratio|ratio|NN|_ calculated|calculate|VBN|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_ total_RNA_rpm.csv.gz|total_rna_rpm.csv.gz|NN|_ is|be|VBZ|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ depth-normalized|depth-normalized|JJ|_ counts|count|NNS|_ for|for|IN|_ every|every|DT|_ genomic|genomic|JJ|_ position|position|NN|_ at|at|IN|_ both|both|DT|_ strans|stran|NNS|_ for|for|IN|_ all|all|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Direct-zol|direct-zol|NN|_ RNA|rna|NN|_ MiniPrep|MiniPrep|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|zymo|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
See|see|VB|_ publication|publication|NN|_ for|for|IN|_ complete|complete|JJ|_ protocol|protocol|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ samples|sample|NNS|_ with|with|IN|_ rRNA|rrna|NN|_ subtraction|subtraction|NN|_ with|with|IN|_ treated|treat|VBN|_ with|with|IN|_ bacterial|bacterial|JJ|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ with|with|IN|_ RNA|rna|NN|_ fragmentation|fragmentation|NN|_ reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ First|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ random|random|JJ|_ primers|primer|NNS|_ and|and|CC|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ enable|enable|VB|_ strand|strand|NN|_ specificity|specificity|NN|_ ,|,|,|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ dUTP|dutp|NN|_ instead|instead|RB|_ of|of|IN|_ dTTP|dttp|NN|_ with|with|IN|_ RNase|rnase|NN|_ H|h|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ ligase|ligase|NN|_ ,|,|,|_ and|and|CC|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ Ends|end|NNS|_ were|be|VBD|_ repaired|repair|VBN|_ with|with|IN|_ T4|t4|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ ,|,|,|_ Klenow|Klenow|NNP|_ DNA|DNA|NNP|_ polymerase|polymerase|NN|_ ,|,|,|_ and|and|CC|_ T4|t4|NN|_ PNK|pnk|NN|_ .|.|.|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ the|the|DT|_ Klenow|Klenow|NNP|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ '|'|''|_ >|>|JJR|_ 5|5|CD|_ '|'|''|_ exo|exo|SYM|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Y-shaped|y-shaped|JJ|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ and|and|CC|_ 9-12|9-12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ primers|primer|NNS|_ with|with|IN|_ multiplexing|multiplex|VBG|_ indexes|index|NNS|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ an|a|DT|_ acrylamide|acrylamide|NN|_ gel|gel|NN|_ and|and|CC|_ submitted|submit|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ at|at|IN|_ the|the|DT|_ MIT|MIT|NNP|_ BioMicro|BioMicro|NNP|_ Center|Center|NNP|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
Separate|separate|JJ|_ E.|e.|FW|_ coli|coli|FW|_ colonies|colony|NNS|_ were|be|VBD|_ picked|pick|VBN|_ from|from|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ for|for|IN|_ each|each|DT|_ replicate|replicate|VBP|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 12-16|12-16|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ and|and|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ fresh|fresh|JJ|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ 3-4|3-4|CD|_ hours|hour|NNS|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.35|0.35|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaker|shaker|NN|_ at|at|IN|_ 200|200|CD|_ RPM|rpm|NN|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ washed|wash|VBN|_ ,|,|,|_ and|and|CC|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ media|media|NNS|_ lacking|lack|VBG|_ glucose|glucose|NN|SUPP .|.|.|_ After|after|IN|_ at|at|IN|_ least|least|JJS|_ 30|30|CD|_ minutes|minute|NNS|_ of|of|IN|_ recovery|recovery|NN|_ Para|para|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ adding|add|VBG|_ arabinose|arabinose|NN|_ to|to|TO|_ 0.2|0.2|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ for|for|IN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ on|on|IN|_ a|a|DT|_ benchtop|benchtop|JJ|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ flash|flash|VB|_ frozen|freeze|VBN|_ in|in|IN|_ lN2|ln2|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ delta|delta|NN|_ _|_|CD|_ mazF|mazf|NN|GEN
plasmid|plasmid|NN|_ :|:|:|_ pBAD30-empty|pbad30-empty|NN|_
ribozero|ribozero|NN|_ :|:|:|_ Yes|yes|UH|_
ercc|ercc|JJ|_ spike-in|spike-in|NN|_ :|:|:|_ No|no|DT|_
time|time|NN|_ induction|induction|NN|_ :|:|:|_ 5|5|CD|_ minutes|minute|NNS|_
Separate|separate|JJ|_ E.|e.|FW|_ coli|coli|FW|_ colonies|colony|NNS|_ were|be|VBD|_ picked|pick|VBN|_ from|from|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ for|for|IN|_ each|each|DT|_ replicate|replicate|VBP|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 12-16|12-16|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ and|and|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ fresh|fresh|JJ|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ 3-4|3-4|CD|_ hours|hour|NNS|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.35|0.35|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaker|shaker|NN|_ at|at|IN|_ 200|200|CD|_ RPM|rpm|NN|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ washed|wash|VBN|_ ,|,|,|_ and|and|CC|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ media|media|NNS|_ lacking|lack|VBG|_ glucose|glucose|NN|SUPP .|.|.|_ After|after|IN|_ at|at|IN|_ least|least|JJS|_ 30|30|CD|_ minutes|minute|NNS|_ of|of|IN|_ recovery|recovery|NN|_ Para|para|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ adding|add|VBG|_ arabinose|arabinose|NN|_ to|to|TO|_ 0.2|0.2|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ for|for|IN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ on|on|IN|_ a|a|DT|_ benchtop|benchtop|JJ|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ flash|flash|VB|_ frozen|freeze|VBN|_ in|in|IN|_ lN2|ln2|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_
Peter|Peter|NNP|_ ,|,|,|_ ,|,|,|_ Culviner|Culviner|NNP|_
Paired-end|paired-end|NN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_ Any|any|DT|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ removed|remove|VBN|_ prior|prior|RB|_ to|to|TO|_ mapping|mapping|NN|_ .|.|.|_
For|for|IN|_ each|each|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ all|all|DT|_ mapped|map|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ at|at|IN|_ all|all|DT|_ aligned|align|VBN|_ positions|position|NNS|_ a|a|DT|_ count|count|NN|_ was|be|VBD|_ added|add|VBN|_ .|.|.|_
Counts|Counts|NNPS|_ were|be|VBD|_ depth|depth|NN|_ normalized|normalize|VBD|_ to|to|TO|_ a|a|DT|_ pseudo-reference|pseudo-reference|NN|_ sample|sample|NN|_ calculated|calculate|VBN|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ using|use|VBG|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ counts|count|NNS|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
For|for|IN|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ ,|,|,|_ counts|count|VBZ|_ at|at|IN|_ all|all|DT|_ positions|position|NNS|_ were|be|VBD|_ log2|log2|NN|_ transformed|transform|VBN|_ and|and|CC|_ a|a|DT|_ cleavage|cleavage|NN|_ ratio|ratio|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ MazF|mazf|NN|_ -|-|:|_ empty|empty|JJ|_ vector|vector|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ assessing|assess|VBG|_ MazF|mazf|NN|_ cleavage|cleavage|NN|_ in|in|IN|_ transcripts|transcript|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ 5m_ribozero_counts_cleavage_ratio.csv.gz|5m_ribozero_counts_cleavage_ratio.csv.gz|NN|_ is|be|VBZ|_ a|a|DT|_ log-transformed|log-transformed|JJ|_ list|list|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ depth-normalized|depth-normalized|JJ|_ counts|count|NNS|_ for|for|IN|_ every|every|DT|_ genomic|genomic|JJ|_ position|position|NN|_ at|at|IN|_ both|both|DT|_ strands|strand|NNS|_ for|for|IN|_ each|each|DT|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ sample|sample|NN|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ average|average|JJ|_ cleavage|cleavage|NN|_ ratio|ratio|NN|_ calculated|calculate|VBN|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_ total_RNA_rpm.csv.gz|total_rna_rpm.csv.gz|NN|_ is|be|VBZ|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ depth-normalized|depth-normalized|JJ|_ counts|count|NNS|_ for|for|IN|_ every|every|DT|_ genomic|genomic|JJ|_ position|position|NN|_ at|at|IN|_ both|both|DT|_ strans|stran|NNS|_ for|for|IN|_ all|all|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Direct-zol|direct-zol|NN|_ RNA|rna|NN|_ MiniPrep|MiniPrep|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|zymo|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
See|see|VB|_ publication|publication|NN|_ for|for|IN|_ complete|complete|JJ|_ protocol|protocol|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ samples|sample|NNS|_ with|with|IN|_ rRNA|rrna|NN|_ subtraction|subtraction|NN|_ with|with|IN|_ treated|treat|VBN|_ with|with|IN|_ bacterial|bacterial|JJ|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ with|with|IN|_ RNA|rna|NN|_ fragmentation|fragmentation|NN|_ reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ First|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ random|random|JJ|_ primers|primer|NNS|_ and|and|CC|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ enable|enable|VB|_ strand|strand|NN|_ specificity|specificity|NN|_ ,|,|,|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ dUTP|dutp|NN|_ instead|instead|RB|_ of|of|IN|_ dTTP|dttp|NN|_ with|with|IN|_ RNase|rnase|NN|_ H|h|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ ligase|ligase|NN|_ ,|,|,|_ and|and|CC|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ Ends|end|NNS|_ were|be|VBD|_ repaired|repair|VBN|_ with|with|IN|_ T4|t4|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ ,|,|,|_ Klenow|Klenow|NNP|_ DNA|DNA|NNP|_ polymerase|polymerase|NN|_ ,|,|,|_ and|and|CC|_ T4|t4|NN|_ PNK|pnk|NN|_ .|.|.|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ the|the|DT|_ Klenow|Klenow|NNP|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ '|'|''|_ >|>|JJR|_ 5|5|CD|_ '|'|''|_ exo|exo|SYM|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Y-shaped|y-shaped|JJ|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ and|and|CC|_ 9-12|9-12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ primers|primer|NNS|_ with|with|IN|_ multiplexing|multiplex|VBG|_ indexes|index|NNS|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ an|a|DT|_ acrylamide|acrylamide|NN|_ gel|gel|NN|_ and|and|CC|_ submitted|submit|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ at|at|IN|_ the|the|DT|_ MIT|MIT|NNP|_ BioMicro|BioMicro|NNP|_ Center|Center|NNP|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
Separate|separate|JJ|_ E.|e.|FW|_ coli|coli|FW|_ colonies|colony|NNS|_ were|be|VBD|_ picked|pick|VBN|_ from|from|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ for|for|IN|_ each|each|DT|_ replicate|replicate|VBP|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 12-16|12-16|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ and|and|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ fresh|fresh|JJ|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ 3-4|3-4|CD|_ hours|hour|NNS|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.35|0.35|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaker|shaker|NN|_ at|at|IN|_ 200|200|CD|_ RPM|rpm|NN|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ washed|wash|VBN|_ ,|,|,|_ and|and|CC|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ media|media|NNS|_ lacking|lack|VBG|_ glucose|glucose|NN|SUPP .|.|.|_ After|after|IN|_ at|at|IN|_ least|least|JJS|_ 30|30|CD|_ minutes|minute|NNS|_ of|of|IN|_ recovery|recovery|NN|_ Para|para|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ adding|add|VBG|_ arabinose|arabinose|NN|_ to|to|TO|_ 0.2|0.2|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ for|for|IN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ on|on|IN|_ a|a|DT|_ benchtop|benchtop|JJ|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ flash|flash|VB|_ frozen|freeze|VBN|_ in|in|IN|_ lN2|ln2|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ delta|delta|NN|_ _|_|CD|_ mazF|mazf|NN|GEN
plasmid|plasmid|NN|_ :|:|:|_ pBAD30-MazF|pbad30-mazf|NN|_
ribozero|ribozero|NN|_ :|:|:|_ Yes|yes|UH|_
ercc|ercc|JJ|_ spike-in|spike-in|NN|_ :|:|:|_ No|no|DT|_
time|time|NN|_ induction|induction|NN|_ :|:|:|_ 5|5|CD|_ minutes|minute|NNS|_
Separate|separate|JJ|_ E.|e.|FW|_ coli|coli|FW|_ colonies|colony|NNS|_ were|be|VBD|_ picked|pick|VBN|_ from|from|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ for|for|IN|_ each|each|DT|_ replicate|replicate|VBP|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 12-16|12-16|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ and|and|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ fresh|fresh|JJ|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ 3-4|3-4|CD|_ hours|hour|NNS|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.35|0.35|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaker|shaker|NN|_ at|at|IN|_ 200|200|CD|_ RPM|rpm|NN|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ washed|wash|VBN|_ ,|,|,|_ and|and|CC|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ media|media|NNS|_ lacking|lack|VBG|_ glucose|glucose|NN|SUPP .|.|.|_ After|after|IN|_ at|at|IN|_ least|least|JJS|_ 30|30|CD|_ minutes|minute|NNS|_ of|of|IN|_ recovery|recovery|NN|_ Para|para|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ adding|add|VBG|_ arabinose|arabinose|NN|_ to|to|TO|_ 0.2|0.2|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ for|for|IN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ on|on|IN|_ a|a|DT|_ benchtop|benchtop|JJ|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ flash|flash|VB|_ frozen|freeze|VBN|_ in|in|IN|_ lN2|ln2|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_
Peter|Peter|NNP|_ ,|,|,|_ ,|,|,|_ Culviner|Culviner|NNP|_
Paired-end|paired-end|NN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_ Any|any|DT|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ removed|remove|VBN|_ prior|prior|RB|_ to|to|TO|_ mapping|mapping|NN|_ .|.|.|_
For|for|IN|_ each|each|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ all|all|DT|_ mapped|map|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ at|at|IN|_ all|all|DT|_ aligned|align|VBN|_ positions|position|NNS|_ a|a|DT|_ count|count|NN|_ was|be|VBD|_ added|add|VBN|_ .|.|.|_
Counts|Counts|NNPS|_ were|be|VBD|_ depth|depth|NN|_ normalized|normalize|VBD|_ to|to|TO|_ a|a|DT|_ pseudo-reference|pseudo-reference|NN|_ sample|sample|NN|_ calculated|calculate|VBN|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ using|use|VBG|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ counts|count|NNS|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
For|for|IN|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ ,|,|,|_ counts|count|VBZ|_ at|at|IN|_ all|all|DT|_ positions|position|NNS|_ were|be|VBD|_ log2|log2|NN|_ transformed|transform|VBN|_ and|and|CC|_ a|a|DT|_ cleavage|cleavage|NN|_ ratio|ratio|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ MazF|mazf|NN|_ -|-|:|_ empty|empty|JJ|_ vector|vector|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ assessing|assess|VBG|_ MazF|mazf|NN|_ cleavage|cleavage|NN|_ in|in|IN|_ transcripts|transcript|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ 5m_ribozero_counts_cleavage_ratio.csv.gz|5m_ribozero_counts_cleavage_ratio.csv.gz|NN|_ is|be|VBZ|_ a|a|DT|_ log-transformed|log-transformed|JJ|_ list|list|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ depth-normalized|depth-normalized|JJ|_ counts|count|NNS|_ for|for|IN|_ every|every|DT|_ genomic|genomic|JJ|_ position|position|NN|_ at|at|IN|_ both|both|DT|_ strands|strand|NNS|_ for|for|IN|_ each|each|DT|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ sample|sample|NN|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ average|average|JJ|_ cleavage|cleavage|NN|_ ratio|ratio|NN|_ calculated|calculate|VBN|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_ total_RNA_rpm.csv.gz|total_rna_rpm.csv.gz|NN|_ is|be|VBZ|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ depth-normalized|depth-normalized|JJ|_ counts|count|NNS|_ for|for|IN|_ every|every|DT|_ genomic|genomic|JJ|_ position|position|NN|_ at|at|IN|_ both|both|DT|_ strans|stran|NNS|_ for|for|IN|_ all|all|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Direct-zol|direct-zol|NN|_ RNA|rna|NN|_ MiniPrep|MiniPrep|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|zymo|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
See|see|VB|_ publication|publication|NN|_ for|for|IN|_ complete|complete|JJ|_ protocol|protocol|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ samples|sample|NNS|_ with|with|IN|_ rRNA|rrna|NN|_ subtraction|subtraction|NN|_ with|with|IN|_ treated|treat|VBN|_ with|with|IN|_ bacterial|bacterial|JJ|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ with|with|IN|_ RNA|rna|NN|_ fragmentation|fragmentation|NN|_ reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ First|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ random|random|JJ|_ primers|primer|NNS|_ and|and|CC|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ enable|enable|VB|_ strand|strand|NN|_ specificity|specificity|NN|_ ,|,|,|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ dUTP|dutp|NN|_ instead|instead|RB|_ of|of|IN|_ dTTP|dttp|NN|_ with|with|IN|_ RNase|rnase|NN|_ H|h|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ ligase|ligase|NN|_ ,|,|,|_ and|and|CC|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ Ends|end|NNS|_ were|be|VBD|_ repaired|repair|VBN|_ with|with|IN|_ T4|t4|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ ,|,|,|_ Klenow|Klenow|NNP|_ DNA|DNA|NNP|_ polymerase|polymerase|NN|_ ,|,|,|_ and|and|CC|_ T4|t4|NN|_ PNK|pnk|NN|_ .|.|.|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ the|the|DT|_ Klenow|Klenow|NNP|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ '|'|''|_ >|>|JJR|_ 5|5|CD|_ '|'|''|_ exo|exo|SYM|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Y-shaped|y-shaped|JJ|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ and|and|CC|_ 9-12|9-12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ primers|primer|NNS|_ with|with|IN|_ multiplexing|multiplex|VBG|_ indexes|index|NNS|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ an|a|DT|_ acrylamide|acrylamide|NN|_ gel|gel|NN|_ and|and|CC|_ submitted|submit|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ at|at|IN|_ the|the|DT|_ MIT|MIT|NNP|_ BioMicro|BioMicro|NNP|_ Center|Center|NNP|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
Separate|separate|JJ|_ E.|e.|FW|_ coli|coli|FW|_ colonies|colony|NNS|_ were|be|VBD|_ picked|pick|VBN|_ from|from|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ for|for|IN|_ each|each|DT|_ replicate|replicate|VBP|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 12-16|12-16|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ and|and|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ fresh|fresh|JJ|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ 3-4|3-4|CD|_ hours|hour|NNS|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.35|0.35|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaker|shaker|NN|_ at|at|IN|_ 200|200|CD|_ RPM|rpm|NN|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ washed|wash|VBN|_ ,|,|,|_ and|and|CC|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ media|media|NNS|_ lacking|lack|VBG|_ glucose|glucose|NN|SUPP .|.|.|_ After|after|IN|_ at|at|IN|_ least|least|JJS|_ 30|30|CD|_ minutes|minute|NNS|_ of|of|IN|_ recovery|recovery|NN|_ Para|para|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ adding|add|VBG|_ arabinose|arabinose|NN|_ to|to|TO|_ 0.2|0.2|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ for|for|IN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ on|on|IN|_ a|a|DT|_ benchtop|benchtop|JJ|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ flash|flash|VB|_ frozen|freeze|VBN|_ in|in|IN|_ lN2|ln2|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ delta|delta|NN|_ _|_|CD|_ mazF|mazf|NN|GEN
plasmid|plasmid|NN|_ :|:|:|_ pBAD30-MazF|pbad30-mazf|NN|_
ribozero|ribozero|NN|_ :|:|:|_ Yes|yes|UH|_
ercc|ercc|JJ|_ spike-in|spike-in|NN|_ :|:|:|_ No|no|DT|_
time|time|NN|_ induction|induction|NN|_ :|:|:|_ 5|5|CD|_ minutes|minute|NNS|_
Separate|separate|JJ|_ E.|e.|FW|_ coli|coli|FW|_ colonies|colony|NNS|_ were|be|VBD|_ picked|pick|VBN|_ from|from|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ for|for|IN|_ each|each|DT|_ replicate|replicate|VBP|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 12-16|12-16|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ and|and|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ fresh|fresh|JJ|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ 3-4|3-4|CD|_ hours|hour|NNS|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.35|0.35|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaker|shaker|NN|_ at|at|IN|_ 200|200|CD|_ RPM|rpm|NN|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ washed|wash|VBN|_ ,|,|,|_ and|and|CC|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ media|media|NNS|_ lacking|lack|VBG|_ glucose|glucose|NN|SUPP .|.|.|_ After|after|IN|_ at|at|IN|_ least|least|JJS|_ 30|30|CD|_ minutes|minute|NNS|_ of|of|IN|_ recovery|recovery|NN|_ Para|para|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ adding|add|VBG|_ arabinose|arabinose|NN|_ to|to|TO|_ 0.2|0.2|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ for|for|IN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ on|on|IN|_ a|a|DT|_ benchtop|benchtop|JJ|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ flash|flash|VB|_ frozen|freeze|VBN|_ in|in|IN|_ lN2|ln2|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_
Peter|Peter|NNP|_ ,|,|,|_ ,|,|,|_ Culviner|Culviner|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ CF|cf|NN|_ patient|patient|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ cystic|cystic|JJ|_ fibrosis|fibrosis|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glycerol|Glycerol|NNP|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|VBP|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ CF|cf|NN|_ patient|patient|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ cystic|cystic|JJ|_ fibrosis|fibrosis|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glycerol|Glycerol|NNP|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|VBP|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ healthy|healthy|JJ|_ child|child|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ control|control|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glycerol|Glycerol|NNP|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ healthy|healthy|JJ|_ child|child|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ control|control|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glycerol|Glycerol|NNP|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ healthy|healthy|JJ|_ child|child|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ control|control|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glycerol|Glycerol|NNP|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ healthy|healthy|JJ|_ child|child|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ control|control|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glycerol|Glycerol|NNP|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ CF|cf|NN|_ patient|patient|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ cystic|cystic|JJ|_ fibrosis|fibrosis|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glucose|glucose|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|VBP|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ CF|cf|NN|_ patient|patient|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ cystic|cystic|JJ|_ fibrosis|fibrosis|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glucose|glucose|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|VBP|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ CF|cf|NN|_ patient|patient|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ cystic|cystic|JJ|_ fibrosis|fibrosis|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glucose|glucose|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|VBP|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ CF|cf|NN|_ patient|patient|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ cystic|cystic|JJ|_ fibrosis|fibrosis|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glucose|glucose|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|VBP|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ healthy|healthy|JJ|_ child|child|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ control|control|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glucose|glucose|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ healthy|healthy|JJ|_ child|child|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ control|control|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glucose|glucose|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ healthy|healthy|JJ|_ child|child|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ control|control|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glucose|glucose|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
Basecalling|Basecalling|NNP|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ one|one|CD|_ modification|modification|NN|_ :|:|:|_ Phase|phase|NN|_ Lock|lock|NN|_ Gel|gel|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|Eppendorf|NNP|_ ,|,|,|_ Westbury|Westbury|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ better|better|JJR|_ separate|separate|JJ|_ organic|organic|JJ|_ and|and|CC|_ aqueous|aqueous|JJ|_ phases|phase|NNS|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ chloroform|chloroform|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ Ambion|Ambion|NNP|_ rDNAse|rDNAse|NNP|_ I|I|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ cleaned|clean|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ the|the|DT|_ RNA|rna|NN|_ ScreenTape|screentape|NN|_ Assay|assay|NN|_ on|on|IN|_ the|the|DT|_ TapeStation|TapeStation|NNP|_ 2200|2200|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ RIN|rin|NN|_ values|value|NNS|_ greater|greater|JJR|_ than|than|IN|_ 8.0|8.0|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ construction|construction|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
RNA-Seq|rna-seq|NN|_
individual|individual|NN|_ :|:|:|_ healthy|healthy|JJ|_ child|child|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ control|control|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glucose|glucose|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
Samuel|Samuel|NNP|_ ,|,|,|_ ,|,|,|_ Miller|Miller|NNP|_
RNA-seq|RNA-seq|NNP|_ data|datum|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ Sakai|Sakai|NNP|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ Subjunc|subjunc|NN|_ aligner|aligner|NN|_ program|program|NN|_ from|from|IN|_ the|the|DT|_ Subread|Subread|NNP|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .4.6|.4.6|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ http://bioinf.wehi.edu.au/subread/|http://bioinf.wehi.edu.au/subread/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ alignment|alignment|NN|_ Bam|bam|UH|_ files|file|NNS|_ were|be|VBD|_ compared|compare|VBN|_ against|against|IN|_ the|the|DT|_ gene|gene|NN|_ annotation|annotation|NN|_ general|general|JJ|_ feature|feature|NN|_ format|format|NN|_ -LRB-|-lrb-|-LRB-|_ GFF|gff|NN|_ -RRB-|-rrb-|-RRB-|_ file|file|NN|_ ,|,|,|_ and|and|CC|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ featureCounts|featureCounts|NNPS|_ tool|tool|NN|_ from|from|IN|_ Subread|Subread|NNP|_ .|.|.|_ The|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ data|datum|NNS|_ of|of|IN|_ the|the|DT|_ expressed|express|VBN|_ genes|gene|NNS|_ was|be|VBD|_ normalized|normalize|VBN|_ for|for|IN|_ RNA|rna|NN|_ composition|composition|NN|_ using|use|VBG|_ the|the|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M|m|NN|_ values|value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.ncbi.nlm.nih.gov/pubmed/20196867|http://www.ncbi.nlm.nih.gov/pubmed/20196867|NN|_ -RRB-|-rrb-|-RRB-|_ from|from|IN|_ the|the|DT|_ Empirical|empirical|JJ|_ analysis|analysis|NN|_ of|of|IN|_ Digital|Digital|NNP|_ Gene|Gene|NNP|_ Expression|expression|NN|_ Data|datum|NNS|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ EdgeR|edger|NN|_ -RRB-|-rrb-|-RRB-|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ https://bioconductor.org/packages/release/bioc/html/edgeR.html|https://bioconductor.org/packages/release/bioc/html/edger.html|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ transformed|transform|VBN|_ to|to|TO|_ log2CPM|log2cpm|NN|_ -LRB-|-lrb-|-LRB-|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ using|use|VBG|_ the|the|DT|_ voom|voom|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.ncbi.nlm.nih.gov/pubmed/24485249|http://www.ncbi.nlm.nih.gov/pubmed/24485249|NN|_ -RRB-|-rrb-|-RRB-|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ LIMMA|limma|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ https://bioconductor.org/packages/release/bioc/html/limma.html|https://bioconductor.org/packages/release/bioc/html/limma.html|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Next|Next|NNP|_ ,|,|,|_ a|a|DT|_ linear|linear|JJ|_ model|model|NN|_ was|be|VBD|_ built|build|VBN|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ using|use|VBG|_ the|the|DT|_ R|r|NN|_ LIMMA|limma|NN|_ package|package|NN|_ and|and|CC|_ statistics|statistics|NNS|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ were|be|VBD|_ computed|compute|VBN|_ .|.|.|_ To|to|TO|_ filter|filter|NN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ ,|,|,|_ two|two|CD|_ fold|fold|JJ|_ or|or|CC|_ three-fold|three-fold|JJ|_ change|change|NN|_ with|with|IN|_ a|a|DT|_ FDR|FDR|NNP|_ ≤|≤|SYM|_ 0.05|0.05|CD|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ threshold|threshold|NN|_ .|.|.|_
Functional|functional|JJ|_ annotation|annotation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ Database|database|NN|_ for|for|IN|_ Annotation|Annotation|NNP|_ ,|,|,|_ Visualization|visualization|NN|_ and|and|CC|_ Integrated|Integrated|NNP|_ Discovery|Discovery|NNP|_ -LRB-|-lrb-|-LRB-|_ DAVID|DAVID|NNP|_ -RRB-|-rrb-|-RRB-|_ Bioinformatics|Bioinformatics|NNP|_ Resources|Resources|NNP|_ 6.7|6.7|CD|_ ,|,|,|_ NIAID|NIAID|NNP|_ ,|,|,|_ NIH|NIH|NNP|_ -LRB-|-lrb-|-LRB-|_ http://david.abcc.ncifcrf.gov|http://david.abcc.ncifcrf.gov|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Total|Total|NNP|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ RNAzol|rnazol|NN|_ RT|rt|NN|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Research|Research|NNP|_ Center|Center|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ following|follow|VBG|_ manufature|manufature|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Contaminating|contaminate|VBG|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ samples|sample|NNS|_ by|by|IN|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ using|use|VBG|_ the|the|DT|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ ;|;|:|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Ribozero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ gram|gram|NN|_ negative|negative|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ protocol|protocol|NN|_ .|.|.|_
PA20|pa20|NN|_ cultures|culture|NNS|_ for|for|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ T-agar|t-agar|JJ|_ with|with|IN|_ and|and|CC|_ without|without|IN|_ added|add|VBN|_ Sulfamethoxazole|Sulfamethoxazole|NNP|_ -|-|:|_ Trimethoprim|Trimethoprim|NNP|_ at|at|IN|_ designated|designate|VBN|_ levels|level|NNS|_ for|for|IN|_ the|the|DT|_ indicated|indicated|JJ|_ times|time|NNS|_ and|and|CC|_ temperatures|temperature|NNS|_ .|.|.|_ Working|work|VBG|_ stocks|stock|NNS|_ were|be|VBD|_ tested|test|VBN|_ and|and|CC|_ maintained|maintain|VBN|_ using|use|VBG|_ LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ formulation|formulation|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ LB|lb|NN|_ agar|agar|NN|_ .|.|.|_ Plasmid|plasmid|NN|_ pSE380|pse380|NN|_ derivatives|derivative|NNS|_ were|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ IPTG|iptg|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
PA20|pa20|NN|_ cultures|culture|NNS|_
RNA-Seq|rna-seq|NN|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ 5|5|CD|_ hr|hr|NN|_
ug/ml|ug/ml|JJ|_ smx|smx|NN|_ /|/|:|_ ug/ml|ug/ml|JJ|_ tm|tm|NN|_ :|:|:|_ 540/108|540/108|CD|_ -LRB-|-lrb-|-LRB-|_ 27x|27x|NN|_ -RRB-|-rrb-|-RRB-|_
PA20|pa20|NN|_ cultures|culture|NNS|_ for|for|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ T-agar|t-agar|JJ|_ with|with|IN|_ and|and|CC|_ without|without|IN|_ added|add|VBN|_ Sulfamethoxazole|Sulfamethoxazole|NNP|_ -|-|:|_ Trimethoprim|Trimethoprim|NNP|_ at|at|IN|_ designated|designate|VBN|_ levels|level|NNS|_ for|for|IN|_ the|the|DT|_ indicated|indicated|JJ|_ times|time|NNS|_ and|and|CC|_ temperatures|temperature|NNS|_ .|.|.|_ Working|work|VBG|_ stocks|stock|NNS|_ were|be|VBD|_ tested|test|VBN|_ and|and|CC|_ maintained|maintain|VBN|_ using|use|VBG|_ LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ formulation|formulation|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ LB|lb|NN|_ agar|agar|NN|_ .|.|.|_ Plasmid|plasmid|NN|_ pSE380|pse380|NN|_ derivatives|derivative|NNS|_ were|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ IPTG|iptg|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
PA20|pa20|NN|_ cultures|culture|NNS|_
Gaylen|Gaylen|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Ulrich|Ulrich|NNP|_
RNA-seq|RNA-seq|NNP|_ data|datum|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ Sakai|Sakai|NNP|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ Subjunc|subjunc|NN|_ aligner|aligner|NN|_ program|program|NN|_ from|from|IN|_ the|the|DT|_ Subread|Subread|NNP|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .4.6|.4.6|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ http://bioinf.wehi.edu.au/subread/|http://bioinf.wehi.edu.au/subread/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ alignment|alignment|NN|_ Bam|bam|UH|_ files|file|NNS|_ were|be|VBD|_ compared|compare|VBN|_ against|against|IN|_ the|the|DT|_ gene|gene|NN|_ annotation|annotation|NN|_ general|general|JJ|_ feature|feature|NN|_ format|format|NN|_ -LRB-|-lrb-|-LRB-|_ GFF|gff|NN|_ -RRB-|-rrb-|-RRB-|_ file|file|NN|_ ,|,|,|_ and|and|CC|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ featureCounts|featureCounts|NNPS|_ tool|tool|NN|_ from|from|IN|_ Subread|Subread|NNP|_ .|.|.|_ The|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ data|datum|NNS|_ of|of|IN|_ the|the|DT|_ expressed|express|VBN|_ genes|gene|NNS|_ was|be|VBD|_ normalized|normalize|VBN|_ for|for|IN|_ RNA|rna|NN|_ composition|composition|NN|_ using|use|VBG|_ the|the|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M|m|NN|_ values|value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.ncbi.nlm.nih.gov/pubmed/20196867|http://www.ncbi.nlm.nih.gov/pubmed/20196867|NN|_ -RRB-|-rrb-|-RRB-|_ from|from|IN|_ the|the|DT|_ Empirical|empirical|JJ|_ analysis|analysis|NN|_ of|of|IN|_ Digital|Digital|NNP|_ Gene|Gene|NNP|_ Expression|expression|NN|_ Data|datum|NNS|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ EdgeR|edger|NN|_ -RRB-|-rrb-|-RRB-|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ https://bioconductor.org/packages/release/bioc/html/edgeR.html|https://bioconductor.org/packages/release/bioc/html/edger.html|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ transformed|transform|VBN|_ to|to|TO|_ log2CPM|log2cpm|NN|_ -LRB-|-lrb-|-LRB-|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ using|use|VBG|_ the|the|DT|_ voom|voom|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.ncbi.nlm.nih.gov/pubmed/24485249|http://www.ncbi.nlm.nih.gov/pubmed/24485249|NN|_ -RRB-|-rrb-|-RRB-|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ LIMMA|limma|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ https://bioconductor.org/packages/release/bioc/html/limma.html|https://bioconductor.org/packages/release/bioc/html/limma.html|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Next|Next|NNP|_ ,|,|,|_ a|a|DT|_ linear|linear|JJ|_ model|model|NN|_ was|be|VBD|_ built|build|VBN|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ using|use|VBG|_ the|the|DT|_ R|r|NN|_ LIMMA|limma|NN|_ package|package|NN|_ and|and|CC|_ statistics|statistics|NNS|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ were|be|VBD|_ computed|compute|VBN|_ .|.|.|_ To|to|TO|_ filter|filter|NN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ ,|,|,|_ two|two|CD|_ fold|fold|JJ|_ or|or|CC|_ three-fold|three-fold|JJ|_ change|change|NN|_ with|with|IN|_ a|a|DT|_ FDR|FDR|NNP|_ ≤|≤|SYM|_ 0.05|0.05|CD|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ threshold|threshold|NN|_ .|.|.|_
Functional|functional|JJ|_ annotation|annotation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ Database|database|NN|_ for|for|IN|_ Annotation|Annotation|NNP|_ ,|,|,|_ Visualization|visualization|NN|_ and|and|CC|_ Integrated|Integrated|NNP|_ Discovery|Discovery|NNP|_ -LRB-|-lrb-|-LRB-|_ DAVID|DAVID|NNP|_ -RRB-|-rrb-|-RRB-|_ Bioinformatics|Bioinformatics|NNP|_ Resources|Resources|NNP|_ 6.7|6.7|CD|_ ,|,|,|_ NIAID|NIAID|NNP|_ ,|,|,|_ NIH|NIH|NNP|_ -LRB-|-lrb-|-LRB-|_ http://david.abcc.ncifcrf.gov|http://david.abcc.ncifcrf.gov|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Total|Total|NNP|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ RNAzol|rnazol|NN|_ RT|rt|NN|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Research|Research|NNP|_ Center|Center|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ following|follow|VBG|_ manufature|manufature|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Contaminating|contaminate|VBG|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ samples|sample|NNS|_ by|by|IN|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ using|use|VBG|_ the|the|DT|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ ;|;|:|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Ribozero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ gram|gram|NN|_ negative|negative|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ protocol|protocol|NN|_ .|.|.|_
PA20|pa20|NN|_ cultures|culture|NNS|_ for|for|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ T-agar|t-agar|JJ|_ with|with|IN|_ and|and|CC|_ without|without|IN|_ added|add|VBN|_ Sulfamethoxazole|Sulfamethoxazole|NNP|_ -|-|:|_ Trimethoprim|Trimethoprim|NNP|_ at|at|IN|_ designated|designate|VBN|_ levels|level|NNS|_ for|for|IN|_ the|the|DT|_ indicated|indicated|JJ|_ times|time|NNS|_ and|and|CC|_ temperatures|temperature|NNS|_ .|.|.|_ Working|work|VBG|_ stocks|stock|NNS|_ were|be|VBD|_ tested|test|VBN|_ and|and|CC|_ maintained|maintain|VBN|_ using|use|VBG|_ LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ formulation|formulation|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ LB|lb|NN|_ agar|agar|NN|_ .|.|.|_ Plasmid|plasmid|NN|_ pSE380|pse380|NN|_ derivatives|derivative|NNS|_ were|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ IPTG|iptg|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
PA20|pa20|NN|_ cultures|culture|NNS|_
RNA-Seq|rna-seq|NN|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ 5|5|CD|_ hr|hr|NN|_
ug/ml|ug/ml|JJ|_ smx|smx|NN|_ /|/|:|_ ug/ml|ug/ml|JJ|_ tm|tm|NN|_ :|:|:|_ 20/4|20/4|CD|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ -RRB-|-rrb-|-RRB-|_
PA20|pa20|NN|_ cultures|culture|NNS|_ for|for|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ T-agar|t-agar|JJ|_ with|with|IN|_ and|and|CC|_ without|without|IN|_ added|add|VBN|_ Sulfamethoxazole|Sulfamethoxazole|NNP|_ -|-|:|_ Trimethoprim|Trimethoprim|NNP|_ at|at|IN|_ designated|designate|VBN|_ levels|level|NNS|_ for|for|IN|_ the|the|DT|_ indicated|indicated|JJ|_ times|time|NNS|_ and|and|CC|_ temperatures|temperature|NNS|_ .|.|.|_ Working|work|VBG|_ stocks|stock|NNS|_ were|be|VBD|_ tested|test|VBN|_ and|and|CC|_ maintained|maintain|VBN|_ using|use|VBG|_ LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ formulation|formulation|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ LB|lb|NN|_ agar|agar|NN|_ .|.|.|_ Plasmid|plasmid|NN|_ pSE380|pse380|NN|_ derivatives|derivative|NNS|_ were|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ IPTG|iptg|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
PA20|pa20|NN|_ cultures|culture|NNS|_
Gaylen|Gaylen|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Ulrich|Ulrich|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yafC|yafc|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yafC|yafc|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yeiE|yeie|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yeiE|yeie|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yiaJ|yiaj|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yiaJ|yiaj|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yieP|yiep|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yieP|yiep|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_ pH5|ph5|NN|_ .5|.5|CD|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_ pH5|ph5|NN|_ .5|.5|CD|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_ pH8|ph8|NN|_ .5|.5|CD|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_ pH8|ph8|NN|_ .5|.5|CD|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ ybaOdeletion|ybaodeletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ ybaO|ybao|NN|_ deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ ybaQ|ybaq|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ ybaQ|ybaq|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ ybiH|ybih|NN|_ deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ ybiH|ybih|NN|_ deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_ pH5|ph5|NN|_ .5|.5|CD|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ ydcI|ydci|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_ pH5|ph5|NN|_ .5|.5|CD|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ ydcI|ydci|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_ pH8|ph8|NN|_ .5|.5|CD|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ ydcI|ydci|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_ pH8|ph8|NN|_ .5|.5|CD|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ ydcI|ydci|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yddM|yddm|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yddM|yddm|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yheO|yheo|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ the|the|DT|_ maximum|maximum|JJ|_ insert|insert|NN|_ size|size|NN|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ after|after|IN|_ trimming|trim|VBG|_ 3|3|CD|_ bp|bp|NN|_ at|at|IN|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_
SAM|SAM|NNP|_ files|file|VBZ|_ generated|generate|VBN|_ from|from|IN|_ bowtie|bowtie|NN|_ ,|,|,|_ then|then|RB|_ ,|,|,|_ were|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ http://cufflinks.cbcb.umd.edu/|http://cufflinks.cbcb.umd.edu/|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cufflinks|Cufflinks|NNP|_ was|be|VBD|_ run|run|VBN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ with|with|IN|_ the|the|DT|_ library|library|NN|_ type|type|NN|_ of|of|IN|_ dUTP|dutp|NN|_ RNA-seq|rna-seq|NN|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ classic-fpkm|classic-fpkm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Three|three|CD|_ milliliters|milliliter|NNS|_ of|of|IN|_ cells|cell|NNS|_ from|from|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mixed|mixed|JJ|_ immediately|immediately|RB|_ by|by|IN|_ vortexing|vortex|VBG|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000g|5000g|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ any|any|DT|_ residual|residual|JJ|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ MRZMB126|mrzmb126|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ for|for|IN|_ the|the|DT|_ removal|removal|NN|_ of|of|IN|_ rRNA|rrna|NN|_ procedure|procedure|NN|_ .|.|.|_ Then|then|RB|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .08098107702|.08098107702|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
medium|medium|NN|_ :|:|:|_ glucose|glucose|NN|SUPP M9|m9|NN|_ minimal|minimal|JJ|_
phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ yheO|yheo|NN|GEN deletion|deletion|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ the|the|DT|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED for|for|IN|_ each|each|DT|_ TF|tf|NN|_ candidate|candidate|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ was|be|VBD|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacteria|bacterium|NNS|_ cells|cell|NNS|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI4|fhi4|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI4|fhi4|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000951835|000951835|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI4|fhi4|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI4|fhi4|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI4|fhi4|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000951835|000951835|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI4|fhi4|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI6|fhi6|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI6|fhi6|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000941895|000941895|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI6|fhi6|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI6|fhi6|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI6|fhi6|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000941895|000941895|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI6|fhi6|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI7|fhi7|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI7|fhi7|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000936245|000936245|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI7|fhi7|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI7|fhi7|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI7|fhi7|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000936245|000936245|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI7|fhi7|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI8|fhi8|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI8|fhi8|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000941395|000941395|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI8|fhi8|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI8|fhi8|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI8|fhi8|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000941395|000941395|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI8|fhi8|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI9|fhi9|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI9|fhi9|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000939195|000939195|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI9|fhi9|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI12|fhi12|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI12|fhi12|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000937275|000937275|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI12|fhi12|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI12|fhi12|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI12|fhi12|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000937275|000937275|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI12|fhi12|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI24|fhi24|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI24|fhi24|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000936225|000936225|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI24|fhi24|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI25|fhi25|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI25|fhi25|CD|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000938995|000938995|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI25|fhi25|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI25|fhi25|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI25|fhi25|CD|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000938995|000938995|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI25|fhi25|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI27|fhi27|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI27|fhi27|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000951875|000951875|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI27|fhi27|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI27|fhi27|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI27|fhi27|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000951875|000951875|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI27|fhi27|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI36|fhi36|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI36|fhi36|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000753215|000753215|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI36|fhi36|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI36|fhi36|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI36|fhi36|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000753215|000753215|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI36|fhi36|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI43|fhi43|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI43|fhi43|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000939755|000939755|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI43|fhi43|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI43|fhi43|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI43|fhi43|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000939755|000939755|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI43|fhi43|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI48|fhi48|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI48|fhi48|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000951915|000951915|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI48|fhi48|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI79|fhi79|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI79|fhi79|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000939955|000939955|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI79|fhi79|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI79|fhi79|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI79|fhi79|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000939955|000939955|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI79|fhi79|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI95|fhi95|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI95|fhi95|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000753275|000753275|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI95|fhi95|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI95|fhi95|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI95|fhi95|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000753275|000753275|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI95|fhi95|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav40|Olav40|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav40|Olav40|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965575|000965575|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav40|Olav40|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav104|Olav104|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav104|Olav104|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000947315|000947315|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav104|Olav104|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav104|Olav104|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav104|Olav104|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000947315|000947315|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav104|Olav104|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav157|Olav157|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav157|Olav157|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965635|000965635|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav157|Olav157|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav157|Olav157|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav157|Olav157|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965635|000965635|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav157|Olav157|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav172|Olav172|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav172|Olav172|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000752975|000752975|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav172|Olav172|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav174|Olav174|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav174|Olav174|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965665|000965665|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav174|Olav174|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav174|Olav174|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav174|Olav174|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965665|000965665|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav174|Olav174|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav178|Olav178|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav178|Olav178|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965555|000965555|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav178|Olav178|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav178|Olav178|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav178|Olav178|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965555|000965555|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav178|Olav178|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav179|Olav179|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav179|Olav179|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965705|000965705|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav179|Olav179|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav179|Olav179|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav179|Olav179|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965705|000965705|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav179|Olav179|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI63|fhi63|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI63|fhi63|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000946755|000946755|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI63|fhi63|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI63|fhi63|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI63|fhi63|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000946755|000946755|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI63|fhi63|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI66|fhi66|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI66|fhi66|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000936475|000936475|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI66|fhi66|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI66|fhi66|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI66|fhi66|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000936475|000936475|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI66|fhi66|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI83|fhi83|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI83|fhi83|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000938695|000938695|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI83|fhi83|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI83|fhi83|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ FHI83|fhi83|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000938695|000938695|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI83|fhi83|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav17|Olav17|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav17|Olav17|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000966935|000966935|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav17|Olav17|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav17|Olav17|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav17|Olav17|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000966935|000966935|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav17|Olav17|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav39|Olav39|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav39|Olav39|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965545|000965545|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav39|Olav39|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav63|Olav63|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav63|Olav63|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965625|000965625|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav63|Olav63|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav63|Olav63|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav63|Olav63|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965625|000965625|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav63|Olav63|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav164|Olav164|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav164|Olav164|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ PVRW00000000|pvrw00000000|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav164|Olav164|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav164|Olav164|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav164|Olav164|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ PVRW00000000|pvrw00000000|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav164|Olav164|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav176|Olav176|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav176|Olav176|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965715|000965715|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav176|Olav176|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav39|Olav39|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav39|Olav39|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965545|000965545|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav39|Olav39|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav173|Olav173|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav173|Olav173|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ Non-HUS|non-hus|JJ|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Induced|induce|VBN|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965655|000965655|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav173|Olav173|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Tagwise|tagwise|JJ|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav176|Olav176|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav176|Olav176|NNP|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus/non-hus|hus/non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ HUS|hus|NN|_
induced/non-induced|induced/non-induced|JJ|_ :|:|:|_ Non-induced|non-induced|JJ|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965715|000965715|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav176|Olav176|NNP|_
The|The|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg/ml|μg/ml|NN|_ .|.|.|_ Both|both|DT|_ cultures|culture|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 5-10|5-10|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNA|rna|NN|_ later|later|RB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Christina|Christina|NNP|_ ,|,|,|_ Gabrielsen|Gabrielsen|NNP|_ ,|,|,|_ Aas|Aas|NNP|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.coli|e.coli|VB|_ K2|k2|NN|_ BW25113|bw25113|NN|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.2|.12.2|CD|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NN|_ K12|k12|NN|_ BW25113|bw25113|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
After|after|IN|_ chilling|chill|VBG|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ each|each|DT|_ 100-ml|100-ml|JJ|_ culture|culture|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 25|25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ ethanol/phenol|ethanol/phenol|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ in|in|IN|_ 95|95|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 7,000|7,000|CD|_ g|g|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ flash-frozen|flash-frozen|JJ|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ .|.|.|_ Two|two|CD|_ independent|independent|JJ|_ cultures|culture|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ mixed|mix|VBN|_ together|together|RB|_ for|for|IN|_ determination|determination|NN|_ of|of|IN|_ transcriptional|transcriptional|JJ|_ profiles|profile|NNS|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ collected|collect|VBN|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientifc|Scientifc|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ and|and|CC|_ cDNA|cdna|NN|_ amplification|amplification|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ SMART-Seq|smart-seq|NN|_ v4|v4|NN|_ Ultra|Ultra|NNP|_ Low|Low|NNP|_ Input|Input|NNP|_ RNA|rna|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Clontech|clontech|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ and|and|CC|_ analyzed|analyze|VBN|_ for|for|IN|_ concentration|concentration|NN|_ ,|,|,|_ size|size|NN|_ distribution|distribution|NN|_ and|and|CC|_ quantification|quantification|NN|_ of|of|IN|_ viable|viable|JJ|_ sequencing|sequencing|NN|_ templates|template|NNS|_ via|via|IN|_ qPCR|qpcr|NN|_ .|.|.|_
To|to|TO|_ generate|generate|VB|_ Illumina-compatible|illumina-compatible|JJ|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ molecular|molecular|JJ|_ indexes|index|NNS|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ each|each|DT|_ library|library|NN|_ ,|,|,|_ allowing|allow|VBG|_ samples|sample|NNS|_ to|to|TO|_ be|be|VB|_ pooled|pool|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ with|with|IN|_ a|a|DT|_ 1|1|CD|_ x|x|CC|_ 50|50|CD|_ bp|bp|NN|_ single-end|single-end|JJ|_ configuration|configuration|NN|_ .|.|.|_ More|more|JJR|_ than|than|IN|_ 250|250|CD|_ million|million|CD|_ reads|read|VBZ|_ were|be|VBD|_ generated|generate|VBN|_ per|per|IN|_ sample|sample|NN|_ ,|,|,|_ and|and|CC|_ at|at|IN|_ least|least|JJS|_ 80|80|CD|_ %|%|NN|_ bases|basis|NNS|_ had|have|VBD|_ quality|quality|NN|_ scores|score|NNS|_ above|above|IN|_ Q30|q30|NN|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ single|single|JJ|_ mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 2429|2429|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ ΔahpC|δahpc|NN|_ double|double|JJ|_ mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 3780|3780|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 3.2|3.2|CD|_ %|%|NN|_ peptone|peptone|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP and|and|CC|_ 1|1|CD|_ %|%|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ early-log|early-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.15|0.15|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|JJ|_ these|these|DT|_ log-phase|log-phase|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 20-fold|20-fold|RB|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ pre-warmed|pre-warmed|JJ|_ ,|,|,|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cultures|culture|NNS|_
Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-ml|200-ml|JJ|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ above|above|JJ|_ cultures|culture|NNS|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ aliquots|aliquot|NNS|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ 100|100|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ aliquots|aliquot|NNS|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ or|or|CC|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ 2429|2429|CD|_
culture|culture|NN|_ temperature|temperature|NN|_ :|:|:|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_
medium|medium|NN|_ :|:|:|_ SB|sb|NN|_ broth|broth|NN|_
Overnight|overnight|NN|_ cultures|culture|NNS|_ of|of|IN|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ single|single|JJ|_ mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 2429|2429|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ ΔahpC|δahpc|NN|_ double|double|JJ|_ mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 3780|3780|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 3.2|3.2|CD|_ %|%|NN|_ peptone|peptone|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP and|and|CC|_ 1|1|CD|_ %|%|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ early-log|early-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.15|0.15|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|JJ|_ these|these|DT|_ log-phase|log-phase|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 20-fold|20-fold|RB|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ pre-warmed|pre-warmed|JJ|_ ,|,|,|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cultures|culture|NNS|_
Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-ml|200-ml|JJ|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ above|above|JJ|_ cultures|culture|NNS|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ aliquots|aliquot|NNS|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ 100|100|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ aliquots|aliquot|NNS|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ or|or|CC|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Yuzhi|Yuzhi|NNP|_ ,|,|,|_ ,|,|,|_ Hong|Hong|NNP|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.coli|e.coli|VB|_ K2|k2|NN|_ BW25113|bw25113|NN|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.2|.12.2|CD|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NN|_ K12|k12|NN|_ BW25113|bw25113|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
After|after|IN|_ chilling|chill|VBG|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ each|each|DT|_ 100-ml|100-ml|JJ|_ culture|culture|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 25|25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ ethanol/phenol|ethanol/phenol|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ in|in|IN|_ 95|95|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 7,000|7,000|CD|_ g|g|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ flash-frozen|flash-frozen|JJ|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ .|.|.|_ Two|two|CD|_ independent|independent|JJ|_ cultures|culture|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ mixed|mix|VBN|_ together|together|RB|_ for|for|IN|_ determination|determination|NN|_ of|of|IN|_ transcriptional|transcriptional|JJ|_ profiles|profile|NNS|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ collected|collect|VBN|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientifc|Scientifc|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ and|and|CC|_ cDNA|cdna|NN|_ amplification|amplification|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ SMART-Seq|smart-seq|NN|_ v4|v4|NN|_ Ultra|Ultra|NNP|_ Low|Low|NNP|_ Input|Input|NNP|_ RNA|rna|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Clontech|clontech|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ and|and|CC|_ analyzed|analyze|VBN|_ for|for|IN|_ concentration|concentration|NN|_ ,|,|,|_ size|size|NN|_ distribution|distribution|NN|_ and|and|CC|_ quantification|quantification|NN|_ of|of|IN|_ viable|viable|JJ|_ sequencing|sequencing|NN|_ templates|template|NNS|_ via|via|IN|_ qPCR|qpcr|NN|_ .|.|.|_
To|to|TO|_ generate|generate|VB|_ Illumina-compatible|illumina-compatible|JJ|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ molecular|molecular|JJ|_ indexes|index|NNS|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ each|each|DT|_ library|library|NN|_ ,|,|,|_ allowing|allow|VBG|_ samples|sample|NNS|_ to|to|TO|_ be|be|VB|_ pooled|pool|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ with|with|IN|_ a|a|DT|_ 1|1|CD|_ x|x|CC|_ 50|50|CD|_ bp|bp|NN|_ single-end|single-end|JJ|_ configuration|configuration|NN|_ .|.|.|_ More|more|JJR|_ than|than|IN|_ 250|250|CD|_ million|million|CD|_ reads|read|VBZ|_ were|be|VBD|_ generated|generate|VBN|_ per|per|IN|_ sample|sample|NN|_ ,|,|,|_ and|and|CC|_ at|at|IN|_ least|least|JJS|_ 80|80|CD|_ %|%|NN|_ bases|basis|NNS|_ had|have|VBD|_ quality|quality|NN|_ scores|score|NNS|_ above|above|IN|_ Q30|q30|NN|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ single|single|JJ|_ mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 2429|2429|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ ΔahpC|δahpc|NN|_ double|double|JJ|_ mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 3780|3780|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 3.2|3.2|CD|_ %|%|NN|_ peptone|peptone|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP and|and|CC|_ 1|1|CD|_ %|%|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ early-log|early-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.15|0.15|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|JJ|_ these|these|DT|_ log-phase|log-phase|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 20-fold|20-fold|RB|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ pre-warmed|pre-warmed|JJ|_ ,|,|,|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cultures|culture|NNS|_
Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-ml|200-ml|JJ|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ above|above|JJ|_ cultures|culture|NNS|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ aliquots|aliquot|NNS|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ 100|100|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ aliquots|aliquot|NNS|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ or|or|CC|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ 3780|3780|CD|_
culture|culture|NN|_ temperature|temperature|NN|_ :|:|:|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_
medium|medium|NN|_ :|:|:|_ SB|sb|NN|_ broth|broth|NN|_
Overnight|overnight|NN|_ cultures|culture|NNS|_ of|of|IN|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ single|single|JJ|_ mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 2429|2429|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ ΔahpC|δahpc|NN|_ double|double|JJ|_ mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 3780|3780|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 3.2|3.2|CD|_ %|%|NN|_ peptone|peptone|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP and|and|CC|_ 1|1|CD|_ %|%|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ early-log|early-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.15|0.15|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|JJ|_ these|these|DT|_ log-phase|log-phase|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 20-fold|20-fold|RB|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ pre-warmed|pre-warmed|JJ|_ ,|,|,|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cultures|culture|NNS|_
Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-ml|200-ml|JJ|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ above|above|JJ|_ cultures|culture|NNS|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ aliquots|aliquot|NNS|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ 100|100|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ aliquots|aliquot|NNS|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ or|or|CC|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Yuzhi|Yuzhi|NNP|_ ,|,|,|_ ,|,|,|_ Hong|Hong|NNP|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.coli|e.coli|VB|_ K2|k2|NN|_ BW25113|bw25113|NN|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.2|.12.2|CD|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NN|_ K12|k12|NN|_ BW25113|bw25113|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
After|after|IN|_ chilling|chill|VBG|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ each|each|DT|_ 100-ml|100-ml|JJ|_ culture|culture|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 25|25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ ethanol/phenol|ethanol/phenol|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ in|in|IN|_ 95|95|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 7,000|7,000|CD|_ g|g|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ flash-frozen|flash-frozen|JJ|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ .|.|.|_ Two|two|CD|_ independent|independent|JJ|_ cultures|culture|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ mixed|mix|VBN|_ together|together|RB|_ for|for|IN|_ determination|determination|NN|_ of|of|IN|_ transcriptional|transcriptional|JJ|_ profiles|profile|NNS|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ collected|collect|VBN|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientifc|Scientifc|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ and|and|CC|_ cDNA|cdna|NN|_ amplification|amplification|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ SMART-Seq|smart-seq|NN|_ v4|v4|NN|_ Ultra|Ultra|NNP|_ Low|Low|NNP|_ Input|Input|NNP|_ RNA|rna|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Clontech|clontech|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ and|and|CC|_ analyzed|analyze|VBN|_ for|for|IN|_ concentration|concentration|NN|_ ,|,|,|_ size|size|NN|_ distribution|distribution|NN|_ and|and|CC|_ quantification|quantification|NN|_ of|of|IN|_ viable|viable|JJ|_ sequencing|sequencing|NN|_ templates|template|NNS|_ via|via|IN|_ qPCR|qpcr|NN|_ .|.|.|_
To|to|TO|_ generate|generate|VB|_ Illumina-compatible|illumina-compatible|JJ|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ molecular|molecular|JJ|_ indexes|index|NNS|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ each|each|DT|_ library|library|NN|_ ,|,|,|_ allowing|allow|VBG|_ samples|sample|NNS|_ to|to|TO|_ be|be|VB|_ pooled|pool|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ with|with|IN|_ a|a|DT|_ 1|1|CD|_ x|x|CC|_ 50|50|CD|_ bp|bp|NN|_ single-end|single-end|JJ|_ configuration|configuration|NN|_ .|.|.|_ More|more|JJR|_ than|than|IN|_ 250|250|CD|_ million|million|CD|_ reads|read|VBZ|_ were|be|VBD|_ generated|generate|VBN|_ per|per|IN|_ sample|sample|NN|_ ,|,|,|_ and|and|CC|_ at|at|IN|_ least|least|JJS|_ 80|80|CD|_ %|%|NN|_ bases|basis|NNS|_ had|have|VBD|_ quality|quality|NN|_ scores|score|NNS|_ above|above|IN|_ Q30|q30|NN|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ single|single|JJ|_ mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 2429|2429|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ ΔahpC|δahpc|NN|_ double|double|JJ|_ mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 3780|3780|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 3.2|3.2|CD|_ %|%|NN|_ peptone|peptone|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP and|and|CC|_ 1|1|CD|_ %|%|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ early-log|early-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.15|0.15|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|JJ|_ these|these|DT|_ log-phase|log-phase|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 20-fold|20-fold|RB|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ pre-warmed|pre-warmed|JJ|_ ,|,|,|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cultures|culture|NNS|_
Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-ml|200-ml|JJ|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ above|above|JJ|_ cultures|culture|NNS|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ aliquots|aliquot|NNS|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ 100|100|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ aliquots|aliquot|NNS|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ or|or|CC|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ 3780|3780|CD|_
culture|culture|NN|_ temperature|temperature|NN|_ :|:|:|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_
medium|medium|NN|_ :|:|:|_ SB|sb|NN|_ broth|broth|NN|_
Overnight|overnight|NN|_ cultures|culture|NNS|_ of|of|IN|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ single|single|JJ|_ mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 2429|2429|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ ΔahpC|δahpc|NN|_ double|double|JJ|_ mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 3780|3780|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 3.2|3.2|CD|_ %|%|NN|_ peptone|peptone|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP and|and|CC|_ 1|1|CD|_ %|%|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ early-log|early-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.15|0.15|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|JJ|_ these|these|DT|_ log-phase|log-phase|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 20-fold|20-fold|RB|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ pre-warmed|pre-warmed|JJ|_ ,|,|,|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cultures|culture|NNS|_
Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-ml|200-ml|JJ|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ above|above|JJ|_ cultures|culture|NNS|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ aliquots|aliquot|NNS|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ 100|100|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ aliquots|aliquot|NNS|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ or|or|CC|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Yuzhi|Yuzhi|NNP|_ ,|,|,|_ ,|,|,|_ Hong|Hong|NNP|_
MiSeq|MiSeq|NNP|_ for|for|IN|_ base|base|NN|_ calling|call|VBG|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ data|datum|NNS|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ V11|v11|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ the|the|DT|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ V0|v0|NN|_ .33|.33|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ against|against|IN|_ E.|E.|NNP|_ 149|149|CD|_ coli|coli|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 2.2.4|2.2.4|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ counts|count|NNS|_ of|of|IN|_ reads|read|VBZ|_ 150|150|CD|_ aligning|align|VBG|_ to|to|TO|_ genomic|genomic|JJ|_ features|feature|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ feaureCounts|feaurecount|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ function|function|NN|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Rsubread|rsubread|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_
Gene|gene|NN|_ annotation|annotation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ EcoCyc|EcoCyc|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Database|database|NN|_ -LRB-|-lrb-|-LRB-|_ https://ecocyc.org/|https://ecocyc.org/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ DESeq2|deseq2|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 1.12.4|1.12.4|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ LP|lp|NN|_ group|group|NN|_ and|and|CC|_ the|the|DT|_ HP|HP|NNP|_ group|group|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Table|Table|NNP|_ of|of|IN|_ read|read|VBN|_ counts|count|NNS|_ with|with|IN|_ genes|gene|NNS|_ as|as|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ as|as|IN|_ columns|column|NNS|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicate|replicate|VB|_ ,|,|,|_ each|each|DT|_ with|with|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Total|total|JJ|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Norgen|Norgen|NNP|_ Biotek|Biotek|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ with|with|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_
The|the|DT|_ lysates|lysate|NNS|_ were|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ gDNA|gdna|NN|_ removal|removal|NN|_ columns|column|NNS|_ and|and|CC|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ for|for|IN|_ Gram-positive|gram-positive|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ the|the|DT|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ RNA|rna|NN|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ independently|independently|RB|_ indexed|index|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ multi-plex|multi-plex|JJ|_ oligos|oligo|NNS|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ at|at|IN|_ equimolar|equimolar|JJ|_ ratios|ratio|NNS|_ before|before|IN|_ they|they|PRP|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reagent|Reagent|NNP|_ Kit|kit|NN|_ v3|v3|NN|_ 600|600|CD|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
tissue|tissue|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_
stimulus|stimulus|NN|_ :|:|:|_ 1|1|CD|_ MPa|mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
Meng|Meng|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
MiSeq|MiSeq|NNP|_ for|for|IN|_ base|base|NN|_ calling|call|VBG|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ data|datum|NNS|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ V11|v11|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ the|the|DT|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ V0|v0|NN|_ .33|.33|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ against|against|IN|_ E.|E.|NNP|_ 149|149|CD|_ coli|coli|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 2.2.4|2.2.4|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ counts|count|NNS|_ of|of|IN|_ reads|read|VBZ|_ 150|150|CD|_ aligning|align|VBG|_ to|to|TO|_ genomic|genomic|JJ|_ features|feature|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ feaureCounts|feaurecount|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ function|function|NN|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Rsubread|rsubread|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_
Gene|gene|NN|_ annotation|annotation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ EcoCyc|EcoCyc|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Database|database|NN|_ -LRB-|-lrb-|-LRB-|_ https://ecocyc.org/|https://ecocyc.org/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ DESeq2|deseq2|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 1.12.4|1.12.4|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ LP|lp|NN|_ group|group|NN|_ and|and|CC|_ the|the|DT|_ HP|HP|NNP|_ group|group|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Table|Table|NNP|_ of|of|IN|_ read|read|VBN|_ counts|count|NNS|_ with|with|IN|_ genes|gene|NNS|_ as|as|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ as|as|IN|_ columns|column|NNS|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicate|replicate|VB|_ ,|,|,|_ each|each|DT|_ with|with|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Total|total|JJ|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Norgen|Norgen|NNP|_ Biotek|Biotek|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ with|with|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_
The|the|DT|_ lysates|lysate|NNS|_ were|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ gDNA|gdna|NN|_ removal|removal|NN|_ columns|column|NNS|_ and|and|CC|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ for|for|IN|_ Gram-positive|gram-positive|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ the|the|DT|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ RNA|rna|NN|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ independently|independently|RB|_ indexed|index|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ multi-plex|multi-plex|JJ|_ oligos|oligo|NNS|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ at|at|IN|_ equimolar|equimolar|JJ|_ ratios|ratio|NNS|_ before|before|IN|_ they|they|PRP|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reagent|Reagent|NNP|_ Kit|kit|NN|_ v3|v3|NN|_ 600|600|CD|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
tissue|tissue|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_
stimulus|stimulus|NN|_ :|:|:|_ 1|1|CD|_ MPa|mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
Meng|Meng|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
MiSeq|MiSeq|NNP|_ for|for|IN|_ base|base|NN|_ calling|call|VBG|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ data|datum|NNS|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ V11|v11|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ the|the|DT|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ V0|v0|NN|_ .33|.33|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ against|against|IN|_ E.|E.|NNP|_ 149|149|CD|_ coli|coli|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 2.2.4|2.2.4|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ counts|count|NNS|_ of|of|IN|_ reads|read|VBZ|_ 150|150|CD|_ aligning|align|VBG|_ to|to|TO|_ genomic|genomic|JJ|_ features|feature|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ feaureCounts|feaurecount|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ function|function|NN|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Rsubread|rsubread|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_
Gene|gene|NN|_ annotation|annotation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ EcoCyc|EcoCyc|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Database|database|NN|_ -LRB-|-lrb-|-LRB-|_ https://ecocyc.org/|https://ecocyc.org/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ DESeq2|deseq2|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 1.12.4|1.12.4|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ LP|lp|NN|_ group|group|NN|_ and|and|CC|_ the|the|DT|_ HP|HP|NNP|_ group|group|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Table|Table|NNP|_ of|of|IN|_ read|read|VBN|_ counts|count|NNS|_ with|with|IN|_ genes|gene|NNS|_ as|as|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ as|as|IN|_ columns|column|NNS|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicate|replicate|VB|_ ,|,|,|_ each|each|DT|_ with|with|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Total|total|JJ|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Norgen|Norgen|NNP|_ Biotek|Biotek|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ with|with|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_
The|the|DT|_ lysates|lysate|NNS|_ were|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ gDNA|gdna|NN|_ removal|removal|NN|_ columns|column|NNS|_ and|and|CC|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ for|for|IN|_ Gram-positive|gram-positive|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ the|the|DT|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ RNA|rna|NN|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ independently|independently|RB|_ indexed|index|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ multi-plex|multi-plex|JJ|_ oligos|oligo|NNS|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ at|at|IN|_ equimolar|equimolar|JJ|_ ratios|ratio|NNS|_ before|before|IN|_ they|they|PRP|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reagent|Reagent|NNP|_ Kit|kit|NN|_ v3|v3|NN|_ 600|600|CD|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
tissue|tissue|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_
stimulus|stimulus|NN|_ :|:|:|_ 1|1|CD|_ MPa|mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
Meng|Meng|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
MiSeq|MiSeq|NNP|_ for|for|IN|_ base|base|NN|_ calling|call|VBG|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ data|datum|NNS|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ V11|v11|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ the|the|DT|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ V0|v0|NN|_ .33|.33|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ against|against|IN|_ E.|E.|NNP|_ 149|149|CD|_ coli|coli|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 2.2.4|2.2.4|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ counts|count|NNS|_ of|of|IN|_ reads|read|VBZ|_ 150|150|CD|_ aligning|align|VBG|_ to|to|TO|_ genomic|genomic|JJ|_ features|feature|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ feaureCounts|feaurecount|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ function|function|NN|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Rsubread|rsubread|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_
Gene|gene|NN|_ annotation|annotation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ EcoCyc|EcoCyc|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Database|database|NN|_ -LRB-|-lrb-|-LRB-|_ https://ecocyc.org/|https://ecocyc.org/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ DESeq2|deseq2|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 1.12.4|1.12.4|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ LP|lp|NN|_ group|group|NN|_ and|and|CC|_ the|the|DT|_ HP|HP|NNP|_ group|group|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Table|Table|NNP|_ of|of|IN|_ read|read|VBN|_ counts|count|NNS|_ with|with|IN|_ genes|gene|NNS|_ as|as|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ as|as|IN|_ columns|column|NNS|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicate|replicate|VB|_ ,|,|,|_ each|each|DT|_ with|with|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Total|total|JJ|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Norgen|Norgen|NNP|_ Biotek|Biotek|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ with|with|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_
The|the|DT|_ lysates|lysate|NNS|_ were|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ gDNA|gdna|NN|_ removal|removal|NN|_ columns|column|NNS|_ and|and|CC|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ for|for|IN|_ Gram-positive|gram-positive|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ the|the|DT|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ RNA|rna|NN|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ independently|independently|RB|_ indexed|index|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ multi-plex|multi-plex|JJ|_ oligos|oligo|NNS|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ at|at|IN|_ equimolar|equimolar|JJ|_ ratios|ratio|NNS|_ before|before|IN|_ they|they|PRP|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reagent|Reagent|NNP|_ Kit|kit|NN|_ v3|v3|NN|_ 600|600|CD|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
tissue|tissue|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_
stimulus|stimulus|NN|_ :|:|:|_ 1|1|CD|_ MPa|mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
Meng|Meng|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
MiSeq|MiSeq|NNP|_ for|for|IN|_ base|base|NN|_ calling|call|VBG|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ data|datum|NNS|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ V11|v11|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ the|the|DT|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ V0|v0|NN|_ .33|.33|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ against|against|IN|_ E.|E.|NNP|_ 149|149|CD|_ coli|coli|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 2.2.4|2.2.4|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ counts|count|NNS|_ of|of|IN|_ reads|read|VBZ|_ 150|150|CD|_ aligning|align|VBG|_ to|to|TO|_ genomic|genomic|JJ|_ features|feature|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ feaureCounts|feaurecount|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ function|function|NN|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Rsubread|rsubread|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_
Gene|gene|NN|_ annotation|annotation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ EcoCyc|EcoCyc|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Database|database|NN|_ -LRB-|-lrb-|-LRB-|_ https://ecocyc.org/|https://ecocyc.org/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ DESeq2|deseq2|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 1.12.4|1.12.4|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ LP|lp|NN|_ group|group|NN|_ and|and|CC|_ the|the|DT|_ HP|HP|NNP|_ group|group|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Table|Table|NNP|_ of|of|IN|_ read|read|VBN|_ counts|count|NNS|_ with|with|IN|_ genes|gene|NNS|_ as|as|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ as|as|IN|_ columns|column|NNS|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicate|replicate|VB|_ ,|,|,|_ each|each|DT|_ with|with|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Total|total|JJ|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Norgen|Norgen|NNP|_ Biotek|Biotek|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ with|with|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_
The|the|DT|_ lysates|lysate|NNS|_ were|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ gDNA|gdna|NN|_ removal|removal|NN|_ columns|column|NNS|_ and|and|CC|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ for|for|IN|_ Gram-positive|gram-positive|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ the|the|DT|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ RNA|rna|NN|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ independently|independently|RB|_ indexed|index|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ multi-plex|multi-plex|JJ|_ oligos|oligo|NNS|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ at|at|IN|_ equimolar|equimolar|JJ|_ ratios|ratio|NNS|_ before|before|IN|_ they|they|PRP|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reagent|Reagent|NNP|_ Kit|kit|NN|_ v3|v3|NN|_ 600|600|CD|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
tissue|tissue|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_
stimulus|stimulus|NN|_ :|:|:|_ Control|Control|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
Meng|Meng|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
MiSeq|MiSeq|NNP|_ for|for|IN|_ base|base|NN|_ calling|call|VBG|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ data|datum|NNS|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ V11|v11|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ the|the|DT|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ V0|v0|NN|_ .33|.33|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ against|against|IN|_ E.|E.|NNP|_ 149|149|CD|_ coli|coli|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 2.2.4|2.2.4|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ counts|count|NNS|_ of|of|IN|_ reads|read|VBZ|_ 150|150|CD|_ aligning|align|VBG|_ to|to|TO|_ genomic|genomic|JJ|_ features|feature|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ feaureCounts|feaurecount|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ function|function|NN|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Rsubread|rsubread|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_
Gene|gene|NN|_ annotation|annotation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ EcoCyc|EcoCyc|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Database|database|NN|_ -LRB-|-lrb-|-LRB-|_ https://ecocyc.org/|https://ecocyc.org/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ DESeq2|deseq2|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 1.12.4|1.12.4|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ LP|lp|NN|_ group|group|NN|_ and|and|CC|_ the|the|DT|_ HP|HP|NNP|_ group|group|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Table|Table|NNP|_ of|of|IN|_ read|read|VBN|_ counts|count|NNS|_ with|with|IN|_ genes|gene|NNS|_ as|as|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ as|as|IN|_ columns|column|NNS|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicate|replicate|VB|_ ,|,|,|_ each|each|DT|_ with|with|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Total|total|JJ|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Norgen|Norgen|NNP|_ Biotek|Biotek|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ with|with|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_
The|the|DT|_ lysates|lysate|NNS|_ were|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ gDNA|gdna|NN|_ removal|removal|NN|_ columns|column|NNS|_ and|and|CC|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ for|for|IN|_ Gram-positive|gram-positive|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ the|the|DT|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ RNA|rna|NN|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ independently|independently|RB|_ indexed|index|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ multi-plex|multi-plex|JJ|_ oligos|oligo|NNS|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ at|at|IN|_ equimolar|equimolar|JJ|_ ratios|ratio|NNS|_ before|before|IN|_ they|they|PRP|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reagent|Reagent|NNP|_ Kit|kit|NN|_ v3|v3|NN|_ 600|600|CD|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
tissue|tissue|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_
stimulus|stimulus|NN|_ :|:|:|_ Control|Control|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
Meng|Meng|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
MiSeq|MiSeq|NNP|_ for|for|IN|_ base|base|NN|_ calling|call|VBG|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ data|datum|NNS|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ V11|v11|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ the|the|DT|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ V0|v0|NN|_ .33|.33|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ against|against|IN|_ E.|E.|NNP|_ 149|149|CD|_ coli|coli|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 2.2.4|2.2.4|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ counts|count|NNS|_ of|of|IN|_ reads|read|VBZ|_ 150|150|CD|_ aligning|align|VBG|_ to|to|TO|_ genomic|genomic|JJ|_ features|feature|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ feaureCounts|feaurecount|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ function|function|NN|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Rsubread|rsubread|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_
Gene|gene|NN|_ annotation|annotation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ EcoCyc|EcoCyc|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Database|database|NN|_ -LRB-|-lrb-|-LRB-|_ https://ecocyc.org/|https://ecocyc.org/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ DESeq2|deseq2|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 1.12.4|1.12.4|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ LP|lp|NN|_ group|group|NN|_ and|and|CC|_ the|the|DT|_ HP|HP|NNP|_ group|group|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Table|Table|NNP|_ of|of|IN|_ read|read|VBN|_ counts|count|NNS|_ with|with|IN|_ genes|gene|NNS|_ as|as|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ as|as|IN|_ columns|column|NNS|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicate|replicate|VB|_ ,|,|,|_ each|each|DT|_ with|with|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Total|total|JJ|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Norgen|Norgen|NNP|_ Biotek|Biotek|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ with|with|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_
The|the|DT|_ lysates|lysate|NNS|_ were|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ gDNA|gdna|NN|_ removal|removal|NN|_ columns|column|NNS|_ and|and|CC|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ for|for|IN|_ Gram-positive|gram-positive|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ the|the|DT|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ RNA|rna|NN|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ independently|independently|RB|_ indexed|index|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ multi-plex|multi-plex|JJ|_ oligos|oligo|NNS|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ at|at|IN|_ equimolar|equimolar|JJ|_ ratios|ratio|NNS|_ before|before|IN|_ they|they|PRP|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reagent|Reagent|NNP|_ Kit|kit|NN|_ v3|v3|NN|_ 600|600|CD|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
tissue|tissue|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_
stimulus|stimulus|NN|_ :|:|:|_ Control|Control|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
Meng|Meng|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
MiSeq|MiSeq|NNP|_ for|for|IN|_ base|base|NN|_ calling|call|VBG|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ data|datum|NNS|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ V11|v11|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ the|the|DT|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ V0|v0|NN|_ .33|.33|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ against|against|IN|_ E.|E.|NNP|_ 149|149|CD|_ coli|coli|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 2.2.4|2.2.4|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ counts|count|NNS|_ of|of|IN|_ reads|read|VBZ|_ 150|150|CD|_ aligning|align|VBG|_ to|to|TO|_ genomic|genomic|JJ|_ features|feature|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ feaureCounts|feaurecount|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ function|function|NN|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Rsubread|rsubread|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_
Gene|gene|NN|_ annotation|annotation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ EcoCyc|EcoCyc|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Database|database|NN|_ -LRB-|-lrb-|-LRB-|_ https://ecocyc.org/|https://ecocyc.org/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ R|r|NN|_ package|package|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ DESeq2|deseq2|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 1.12.4|1.12.4|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ LP|lp|NN|_ group|group|NN|_ and|and|CC|_ the|the|DT|_ HP|HP|NNP|_ group|group|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Table|Table|NNP|_ of|of|IN|_ read|read|VBN|_ counts|count|NNS|_ with|with|IN|_ genes|gene|NNS|_ as|as|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ as|as|IN|_ columns|column|NNS|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicate|replicate|VB|_ ,|,|,|_ each|each|DT|_ with|with|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Total|total|JJ|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Norgen|Norgen|NNP|_ Biotek|Biotek|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ with|with|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_
The|the|DT|_ lysates|lysate|NNS|_ were|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ gDNA|gdna|NN|_ removal|removal|NN|_ columns|column|NNS|_ and|and|CC|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ for|for|IN|_ Gram-positive|gram-positive|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ the|the|DT|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ RNA|rna|NN|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ independently|independently|RB|_ indexed|index|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ multi-plex|multi-plex|JJ|_ oligos|oligo|NNS|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ at|at|IN|_ equimolar|equimolar|JJ|_ ratios|ratio|NNS|_ before|before|IN|_ they|they|PRP|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reagent|Reagent|NNP|_ Kit|kit|NN|_ v3|v3|NN|_ 600|600|CD|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
tissue|tissue|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_
stimulus|stimulus|NN|_ :|:|:|_ Control|Control|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
Meng|Meng|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ with|with|IN|_ bowtie2|bowtie2|NN|_
Read|read|VBP|_ counts|count|NNS|_ per|per|IN|_ gene|gene|NN|_ determined|determine|VBN|_ using|use|VBG|_ HTseq|htseq|NN|_ count|count|NN|_ before|before|IN|_ normalized|normalize|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
PCA|pca|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ top|top|JJ|_ 500|500|CD|_ genes|gene|NNS|_ with|with|IN|_ the|the|DT|_ most|most|RBS|_ variations|variation|NNS|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ txt|txt|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ profiles|profile|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ The|the|DT|_ xlsx|xlsx|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ PC1|pc1|NN|_ and|and|CC|_ PC2|pc2|NN|_ values|value|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
After|after|IN|_ exposed|expose|VBN|_ under|under|IN|_ the|the|DT|_ red|red|JJ|_ light|light|NN|_ with|with|IN|_ a|a|DT|_ specific|specific|JJ|_ ON/OFF|on/off|NN|_ frequency|frequency|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ sampled|sample|VBN|_ and|and|CC|_ the|the|DT|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAprep|rnaprep|NN|_ pure|pure|JJ|_ Cell/Bacteria|Cell/Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ TIANGEN|TIANGEN|NNP|_ ,|,|,|_ DP430|dp430|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ preserved|preserve|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pLCenvZ|plcenvz|NN|_ ,|,|,|_ pPCB|ppcb|NN|_ -LRB-|-lrb-|-LRB-|_ wild|wild|JJ|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ JW3367|jw3367|NN|_
input|input|NN|_ signal|signal|NN|_ frequency|frequency|NN|_ :|:|:|_ 1/600|1/600|CD|_ Hz|hz|NN|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
Zhi|Zhi|NNP|_ ,|,|,|_ ,|,|,|_ Liang|Liang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ with|with|IN|_ bowtie2|bowtie2|NN|_
Read|read|VBP|_ counts|count|NNS|_ per|per|IN|_ gene|gene|NN|_ determined|determine|VBN|_ using|use|VBG|_ HTseq|htseq|NN|_ count|count|NN|_ before|before|IN|_ normalized|normalize|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
PCA|pca|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ top|top|JJ|_ 500|500|CD|_ genes|gene|NNS|_ with|with|IN|_ the|the|DT|_ most|most|RBS|_ variations|variation|NNS|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ txt|txt|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ profiles|profile|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ The|the|DT|_ xlsx|xlsx|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ PC1|pc1|NN|_ and|and|CC|_ PC2|pc2|NN|_ values|value|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
After|after|IN|_ exposed|expose|VBN|_ under|under|IN|_ the|the|DT|_ red|red|JJ|_ light|light|NN|_ with|with|IN|_ a|a|DT|_ specific|specific|JJ|_ ON/OFF|on/off|NN|_ frequency|frequency|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ sampled|sample|VBN|_ and|and|CC|_ the|the|DT|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAprep|rnaprep|NN|_ pure|pure|JJ|_ Cell/Bacteria|Cell/Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ TIANGEN|TIANGEN|NNP|_ ,|,|,|_ DP430|dp430|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ preserved|preserve|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pLCenvZ|plcenvz|NN|_ ,|,|,|_ pPCB|ppcb|NN|_ -LRB-|-lrb-|-LRB-|_ wild|wild|JJ|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ JW3367|jw3367|NN|_
input|input|NN|_ signal|signal|NN|_ frequency|frequency|NN|_ :|:|:|_ 1/900|1/900|CD|_ Hz|hz|NN|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
Zhi|Zhi|NNP|_ ,|,|,|_ ,|,|,|_ Liang|Liang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ with|with|IN|_ bowtie2|bowtie2|NN|_
Read|read|VBP|_ counts|count|NNS|_ per|per|IN|_ gene|gene|NN|_ determined|determine|VBN|_ using|use|VBG|_ HTseq|htseq|NN|_ count|count|NN|_ before|before|IN|_ normalized|normalize|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
PCA|pca|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ top|top|JJ|_ 500|500|CD|_ genes|gene|NNS|_ with|with|IN|_ the|the|DT|_ most|most|RBS|_ variations|variation|NNS|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ txt|txt|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ profiles|profile|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ The|the|DT|_ xlsx|xlsx|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ PC1|pc1|NN|_ and|and|CC|_ PC2|pc2|NN|_ values|value|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
After|after|IN|_ exposed|expose|VBN|_ under|under|IN|_ the|the|DT|_ red|red|JJ|_ light|light|NN|_ with|with|IN|_ a|a|DT|_ specific|specific|JJ|_ ON/OFF|on/off|NN|_ frequency|frequency|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ sampled|sample|VBN|_ and|and|CC|_ the|the|DT|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAprep|rnaprep|NN|_ pure|pure|JJ|_ Cell/Bacteria|Cell/Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ TIANGEN|TIANGEN|NNP|_ ,|,|,|_ DP430|dp430|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ preserved|preserve|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pLCenvZ|plcenvz|NN|_ ,|,|,|_ pPCB|ppcb|NN|_ -LRB-|-lrb-|-LRB-|_ wild|wild|JJ|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ JW3367|jw3367|NN|_
input|input|NN|_ signal|signal|NN|_ frequency|frequency|NN|_ :|:|:|_ 1/3600|1/3600|CD|_ Hz|hz|NN|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
Zhi|Zhi|NNP|_ ,|,|,|_ ,|,|,|_ Liang|Liang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ with|with|IN|_ bowtie2|bowtie2|NN|_
Read|read|VBP|_ counts|count|NNS|_ per|per|IN|_ gene|gene|NN|_ determined|determine|VBN|_ using|use|VBG|_ HTseq|htseq|NN|_ count|count|NN|_ before|before|IN|_ normalized|normalize|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
PCA|pca|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ top|top|JJ|_ 500|500|CD|_ genes|gene|NNS|_ with|with|IN|_ the|the|DT|_ most|most|RBS|_ variations|variation|NNS|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ txt|txt|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ profiles|profile|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ The|the|DT|_ xlsx|xlsx|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ PC1|pc1|NN|_ and|and|CC|_ PC2|pc2|NN|_ values|value|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
After|after|IN|_ exposed|expose|VBN|_ under|under|IN|_ the|the|DT|_ red|red|JJ|_ light|light|NN|_ with|with|IN|_ a|a|DT|_ specific|specific|JJ|_ ON/OFF|on/off|NN|_ frequency|frequency|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ sampled|sample|VBN|_ and|and|CC|_ the|the|DT|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAprep|rnaprep|NN|_ pure|pure|JJ|_ Cell/Bacteria|Cell/Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ TIANGEN|TIANGEN|NNP|_ ,|,|,|_ DP430|dp430|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ preserved|preserve|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pLCenvZM|plcenvzm|NN|_ ,|,|,|_ pPCB|ppcb|NN|_ -LRB-|-lrb-|-LRB-|_ mutation|mutation|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ JW3367|jw3367|NN|_
input|input|NN|_ signal|signal|NN|_ frequency|frequency|NN|_ :|:|:|_ 1/600|1/600|CD|_ Hz|hz|NN|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
Zhi|Zhi|NNP|_ ,|,|,|_ ,|,|,|_ Liang|Liang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ with|with|IN|_ bowtie2|bowtie2|NN|_
Read|read|VBP|_ counts|count|NNS|_ per|per|IN|_ gene|gene|NN|_ determined|determine|VBN|_ using|use|VBG|_ HTseq|htseq|NN|_ count|count|NN|_ before|before|IN|_ normalized|normalize|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
PCA|pca|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ top|top|JJ|_ 500|500|CD|_ genes|gene|NNS|_ with|with|IN|_ the|the|DT|_ most|most|RBS|_ variations|variation|NNS|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ txt|txt|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ profiles|profile|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ The|the|DT|_ xlsx|xlsx|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ PC1|pc1|NN|_ and|and|CC|_ PC2|pc2|NN|_ values|value|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
After|after|IN|_ exposed|expose|VBN|_ under|under|IN|_ the|the|DT|_ red|red|JJ|_ light|light|NN|_ with|with|IN|_ a|a|DT|_ specific|specific|JJ|_ ON/OFF|on/off|NN|_ frequency|frequency|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ sampled|sample|VBN|_ and|and|CC|_ the|the|DT|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAprep|rnaprep|NN|_ pure|pure|JJ|_ Cell/Bacteria|Cell/Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ TIANGEN|TIANGEN|NNP|_ ,|,|,|_ DP430|dp430|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ preserved|preserve|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pLCenvZM|plcenvzm|NN|_ ,|,|,|_ pPCB|ppcb|NN|_ -LRB-|-lrb-|-LRB-|_ mutation|mutation|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ JW3367|jw3367|NN|_
input|input|NN|_ signal|signal|NN|_ frequency|frequency|NN|_ :|:|:|_ 1/900|1/900|CD|_ Hz|hz|NN|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
Zhi|Zhi|NNP|_ ,|,|,|_ ,|,|,|_ Liang|Liang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ with|with|IN|_ bowtie2|bowtie2|NN|_
Read|read|VBP|_ counts|count|NNS|_ per|per|IN|_ gene|gene|NN|_ determined|determine|VBN|_ using|use|VBG|_ HTseq|htseq|NN|_ count|count|NN|_ before|before|IN|_ normalized|normalize|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
PCA|pca|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ top|top|JJ|_ 500|500|CD|_ genes|gene|NNS|_ with|with|IN|_ the|the|DT|_ most|most|RBS|_ variations|variation|NNS|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ txt|txt|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ profiles|profile|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ The|the|DT|_ xlsx|xlsx|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ PC1|pc1|NN|_ and|and|CC|_ PC2|pc2|NN|_ values|value|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
After|after|IN|_ exposed|expose|VBN|_ under|under|IN|_ the|the|DT|_ red|red|JJ|_ light|light|NN|_ with|with|IN|_ a|a|DT|_ specific|specific|JJ|_ ON/OFF|on/off|NN|_ frequency|frequency|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ sampled|sample|VBN|_ and|and|CC|_ the|the|DT|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAprep|rnaprep|NN|_ pure|pure|JJ|_ Cell/Bacteria|Cell/Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ TIANGEN|TIANGEN|NNP|_ ,|,|,|_ DP430|dp430|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ preserved|preserve|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pLCenvZM|plcenvzm|NN|_ ,|,|,|_ pPCB|ppcb|NN|_ -LRB-|-lrb-|-LRB-|_ mutation|mutation|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ JW3367|jw3367|NN|_
input|input|NN|_ signal|signal|NN|_ frequency|frequency|NN|_ :|:|:|_ 1/1200|1/1200|CD|_ Hz|hz|NN|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
Zhi|Zhi|NNP|_ ,|,|,|_ ,|,|,|_ Liang|Liang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ with|with|IN|_ bowtie2|bowtie2|NN|_
Read|read|VBP|_ counts|count|NNS|_ per|per|IN|_ gene|gene|NN|_ determined|determine|VBN|_ using|use|VBG|_ HTseq|htseq|NN|_ count|count|NN|_ before|before|IN|_ normalized|normalize|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
PCA|pca|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ top|top|JJ|_ 500|500|CD|_ genes|gene|NNS|_ with|with|IN|_ the|the|DT|_ most|most|RBS|_ variations|variation|NNS|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ txt|txt|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ profiles|profile|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ The|the|DT|_ xlsx|xlsx|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ PC1|pc1|NN|_ and|and|CC|_ PC2|pc2|NN|_ values|value|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
After|after|IN|_ exposed|expose|VBN|_ under|under|IN|_ the|the|DT|_ red|red|JJ|_ light|light|NN|_ with|with|IN|_ a|a|DT|_ specific|specific|JJ|_ ON/OFF|on/off|NN|_ frequency|frequency|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ sampled|sample|VBN|_ and|and|CC|_ the|the|DT|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAprep|rnaprep|NN|_ pure|pure|JJ|_ Cell/Bacteria|Cell/Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ TIANGEN|TIANGEN|NNP|_ ,|,|,|_ DP430|dp430|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ preserved|preserve|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pLCenvZM|plcenvzm|NN|_ ,|,|,|_ pPCB|ppcb|NN|_ -LRB-|-lrb-|-LRB-|_ mutation|mutation|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ JW3367|jw3367|NN|_
input|input|NN|_ signal|signal|NN|_ frequency|frequency|NN|_ :|:|:|_ 1/2400|1/2400|CD|_ Hz|hz|NN|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
Zhi|Zhi|NNP|_ ,|,|,|_ ,|,|,|_ Liang|Liang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ with|with|IN|_ bowtie2|bowtie2|NN|_
Read|read|VBP|_ counts|count|NNS|_ per|per|IN|_ gene|gene|NN|_ determined|determine|VBN|_ using|use|VBG|_ HTseq|htseq|NN|_ count|count|NN|_ before|before|IN|_ normalized|normalize|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
PCA|pca|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ top|top|JJ|_ 500|500|CD|_ genes|gene|NNS|_ with|with|IN|_ the|the|DT|_ most|most|RBS|_ variations|variation|NNS|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ txt|txt|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ profiles|profile|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ The|the|DT|_ xlsx|xlsx|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ PC1|pc1|NN|_ and|and|CC|_ PC2|pc2|NN|_ values|value|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
After|after|IN|_ exposed|expose|VBN|_ under|under|IN|_ the|the|DT|_ red|red|JJ|_ light|light|NN|_ with|with|IN|_ a|a|DT|_ specific|specific|JJ|_ ON/OFF|on/off|NN|_ frequency|frequency|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ sampled|sample|VBN|_ and|and|CC|_ the|the|DT|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAprep|rnaprep|NN|_ pure|pure|JJ|_ Cell/Bacteria|Cell/Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ TIANGEN|TIANGEN|NNP|_ ,|,|,|_ DP430|dp430|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ preserved|preserve|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pLCenvZM|plcenvzm|NN|_ ,|,|,|_ pPCB|ppcb|NN|_ -LRB-|-lrb-|-LRB-|_ mutation|mutation|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ JW3367|jw3367|NN|_
input|input|NN|_ signal|signal|NN|_ frequency|frequency|NN|_ :|:|:|_ 1/3600|1/3600|CD|_ Hz|hz|NN|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
BW25113|bw25113|NN|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Chloramphenicol|chloramphenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 170|170|CD|_ ng/μl|ng/μl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ reach|reach|VB|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ LED|LED|NNP|_ tube|tube|NN|_ was|be|VBD|_ screwed|screw|VBN|_ into|into|IN|_ the|the|DT|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ and|and|CC|_ connected|connect|VBN|_ with|with|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ power|power|NN|_ of|of|IN|_ the|the|DT|_ control|control|NN|_ box|box|NN|_ was|be|VBD|_ turned|turn|VBN|_ on|on|RB|_ and|and|CC|_ the|the|DT|_ LED|lead|VBN|_ frequency|frequency|NN|_ input|input|NN|_ was|be|VBD|_ generated|generate|VBN|_ .|.|.|_ At|at|IN|_ last|last|JJ|_ ,|,|,|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ with|with|IN|_ LED|lead|VBN|_ tube|tube|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ the|the|DT|_ Thermomixer|Thermomixer|NNP|_ comfort|comfort|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 650|650|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ hours|hour|NNS|_ .|.|.|_
Zhi|Zhi|NNP|_ ,|,|,|_ ,|,|,|_ Liang|Liang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.7|1.7|CD|_
Paired-end|paired-end|NN|_ reads|read|VBZ|_ were|be|VBD|_ merged|merge|VBN|_ to|to|TO|_ single|single|JJ|_ end|end|NN|_ fasta|fasta|NN|_ reads|read|VBZ|_ by|by|IN|_ usin|usin|NN|_ FlASh|flash|NN|_ software|software|NN|_ v1|v1|NN|_ .2.11|.2.11|CD|_
Labled|Labled|NNP|_ transcript|transcript|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ merged|merged|JJ|_ single|single|JJ|_ end|end|NN|_ reads|read|VBZ|_ and|and|CC|_ processed|process|VBN|_ to|to|TO|_ paired-end|paired-end|JJ|_ reads|read|VBZ|_ again|again|RB|_ by|by|IN|_ custom|custom|NN|_ program|program|NN|_ scripts|script|NNS|_
Extracted|extract|VBN|_ paired-end|paired-end|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ E.coli|e.coli|JJ|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 00913.3|00913.3|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ v2|v2|NN|_ .3.4.1|.3.4.1|CD|_ ,|,|,|_ and|and|CC|_ single|single|JJ|_ end|end|NN|_ full|full|JJ|_ length|length|NN|_ sequence|sequence|NN|_ was|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ the|the|DT|_ paried-end|paried-end|JJ|_ data|datum|NNS|_ by|by|IN|_ custome|custome|NN|_ transcripts|transcript|NNS|_ and|and|CC|_ Bowtie2|bowtie2|NN|_ .|.|.|_
rRNA|rrna|NN|_ transcripts|transcript|NNS|_ were|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ TSSs|tsss|NNS|_ ,|,|,|_ TTSs|ttss|NNS|_ and|and|CC|_ overlap|overlap|VBP|_ TTSs|ttss|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ remaining|remain|VBG|_ data|datum|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|MG1655|NNP|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wig|wig|NN|_ files|file|NNS|_
For|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ samples|sample|NNS|_ ,|,|,|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 0.5|0.5|CD|_ volume|volume|NN|_ of|of|IN|_ cold|cold|JJ|_ Stop|stop|NN|_ Buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ immediately|immediately|RB|_ to|to|TO|_ the|the|DT|_ culture|culture|NN|_ medium|medium|NN|_ before|before|IN|_ harvest|harvest|NN|_ and|and|CC|_ stay|stay|VB|_ on|on|IN|_ the|the|DT|_ ice|ice|NN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 6,000|6,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ thoroughly|thoroughly|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ μl|μl|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ solution|solution|NN|_ -LSB-|-lsb-|-LRB-|_ 2|2|CD|_ mg/ml|mg/ml|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 2|2|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TRIzol|trizol|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ 15596|15596|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ following|follow|VBG|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ ChIP-seq|ChIP-seq|NNP|_ samples|sample|NNS|_ ,|,|,|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ with|with|IN|_ continued|continued|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ before|before|IN|_ quenching|quench|VBG|_ with|with|IN|_ glycine|glycine|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ lysed|lyse|VBN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ sheared|shear|VBN|_ by|by|IN|_ sonication|sonication|NN|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ and|and|CC|_ RNase|rnase|NN|_ A.|a.|NN|_ Antibody|antibody|NN|_ against|against|IN|_ RNAP|rnap|NN|_ β|β|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ target|target|NN|_ DNA|dna|NN|_ enrichment|enrichment|NN|_ .|.|.|_
A|a|DT|_ new|new|JJ|_ RNA-seq|rna-seq|NN|_ method|method|NN|_ SEnd-seq|send-seq|NN|_ was|be|VBD|_ developed|develop|VBN|_ and|and|CC|_ used|use|VBN|_ to|to|TO|_ prepare|prepare|VB|_ the|the|DT|_ SEnd-seq|send-seq|JJ|_ library|library|NN|_ ,|,|,|_ standard|standard|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ RS-122-2101|rs-122-2101|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ ChIP-seq|ChIP-seq|NNP|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ II|ii|CD|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ ,|,|,|_ E7645|e7645|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ ChIP|chip|NN|_ DNA|dna|NN|_ enrichment|enrichment|NN|_ .|.|.|_ For|for|IN|_ SEnd|send|VB|_ _|_|SYM|_ seq|seq|NN|_ ,|,|,|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ RNA|rna|NN|_ adaptor|adaptor|NN|_ -LRB-|-lrb-|-LRB-|_ /|/|:|_ 5Phos/rNrNrN|5phos/rnrnrn|NN|_ rNrArArCrCrUrGrCrUrArUrCrArArCrUrG/3ddC|rnrararcrcrurgrcrurarurcrararcrurg/3ddc|NN|_ /|/|:|_ or|or|CC|_ /|/|:|_ 5Phos/rNrNrN|5phos/rnrnrn|NN|_ rNrGrCrUrUrCrCrUrGrCrUrArUrCrArArCrUrG/3ddC|rnrgrcrururcrcrurgrcrurarurcrararcrurg/3ddc|NN|_ /|/|:|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ both|both|DT|_ adaptors|adaptor|NNS|_ were|be|VBD|_ used|use|VBN|_ if|if|IN|_ two|two|CD|_ different|different|JJ|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ together|together|RB|_ for|for|IN|_ library|library|NN|_ preparation|preparation|NN|_ -LRB-|-lrb-|-LRB-|_ Log|log|NN|_ phase|phase|NN|_ samples|sample|NNS|_ used|use|VBD|_ the|the|DT|_ first|first|JJ|_ one|one|CD|_ and|and|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase samples|sample|NNS|_ used|use|VBD|_ the|the|DT|_ second|second|JJ|_ one|one|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ ligated|ligate|VBN|_ RNA|rna|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ cDNA|cdna|NN|_ with|with|IN|_ the|the|DT|_ same|same|JJ|_ Biotinylated|biotinylate|VBN|_ RT|rt|NN|_ primer|primer|NN|_ -LRB-|-lrb-|-LRB-|_ 5GGGCAG|5gggcag|NN|_ T/iBiodT/GATAGCAGG|t/ibiodt/gatagcagg|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ rRNA|rrna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ For|for|IN|_ ChIP-seq|ChIP-seq|NNP|_ ,|,|,|_ the|the|DT|_ enriched|enriched|JJ|_ ChIP|chip|NN|_ DNA|dna|NN|_ and|and|CC|_ input|input|NN|_ DNA|dna|NN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ II|ii|CD|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 10|10|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.4|7.4|CD|_ -RRB-|-rrb-|-RRB-|_ under|under|IN|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ temperature-sensitive|temperature-sensitive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ mutant|mutant|JJ|_ E.coli|e.coli|NN|_ strain|strain|NN|_ -LSB-|-lsb-|-LRB-|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ for|for|IN|_ normal|normal|JJ|_ culture|culture|NN|_ and|and|CC|_ shift|shift|NN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ to|to|TO|_ deactive|deactive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|JJ|_ cell|cell|NN|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ pnp|pnp|NN|GEN knoctout|knoctout|NN|_ ,|,|,|_ rnb|rnb|NN|GEN knoctout|knoctout|NN|_ and|and|CC|_ rnr|rnr|NN|GEN knoct|knoct|NN|_ out|out|IN|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ and|and|CC|_ ChIP-seq|chip-seq|JJ|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ when|when|WRB|_ the|the|DT|_ growth|growth|NN|_ stage|stage|NN|_ of|of|IN|_ indicated|indicate|VBN|_ cells|cell|NNS|_ reached|reach|VBD|_ to|to|TO|_ log|log|VB|_ phase|phase|NN|_ or|or|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ mutation|mutation|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ or|or|CC|_ shifted|shift|VBN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ in|in|IN|_ water|water|NN|_ bath|bath|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ to|to|TO|_ deactivate|deactivate|VB|_ RNase|rnase|NN|_ E|e|NN|_ .|.|.|_ In|in|IN|_ order|order|NN|_ to|to|TO|_ inactive|inactive|JJ|_ the|the|DT|_ rho|rho|NN|GEN activity|activity|NN|_ ,|,|,|_ the|the|DT|_ wild|wild|JJ|_ type|type|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ 50|50|CD|_ μg/ml|μg/ml|NN|_ bicyclomycin|bicyclomycin|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ at|at|IN|_ indicated|indicated|JJ|_ growth|growth|NN|_ condition|condition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_
treatment|treatment|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_
strain|strain|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 10|10|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.4|7.4|CD|_ -RRB-|-rrb-|-RRB-|_ under|under|IN|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ temperature-sensitive|temperature-sensitive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ mutant|mutant|JJ|_ E.coli|e.coli|NN|_ strain|strain|NN|_ -LSB-|-lsb-|-LRB-|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ for|for|IN|_ normal|normal|JJ|_ culture|culture|NN|_ and|and|CC|_ shift|shift|NN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ to|to|TO|_ deactive|deactive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|JJ|_ cell|cell|NN|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ pnp|pnp|NN|GEN knoctout|knoctout|NN|_ ,|,|,|_ rnb|rnb|NN|GEN knoctout|knoctout|NN|_ and|and|CC|_ rnr|rnr|NN|GEN knoct|knoct|NN|_ out|out|IN|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ and|and|CC|_ ChIP-seq|chip-seq|JJ|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ when|when|WRB|_ the|the|DT|_ growth|growth|NN|_ stage|stage|NN|_ of|of|IN|_ indicated|indicate|VBN|_ cells|cell|NNS|_ reached|reach|VBD|_ to|to|TO|_ log|log|VB|_ phase|phase|NN|_ or|or|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ mutation|mutation|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ or|or|CC|_ shifted|shift|VBN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ in|in|IN|_ water|water|NN|_ bath|bath|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ to|to|TO|_ deactivate|deactivate|VB|_ RNase|rnase|NN|_ E|e|NN|_ .|.|.|_ In|in|IN|_ order|order|NN|_ to|to|TO|_ inactive|inactive|JJ|_ the|the|DT|_ rho|rho|NN|GEN activity|activity|NN|_ ,|,|,|_ the|the|DT|_ wild|wild|JJ|_ type|type|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ 50|50|CD|_ μg/ml|μg/ml|NN|_ bicyclomycin|bicyclomycin|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ at|at|IN|_ indicated|indicated|JJ|_ growth|growth|NN|_ condition|condition|NN|_ .|.|.|_
Xiangwu|xiangwu|NN|_ ,|,|,|_ ,|,|,|_ Ju|ju|NN|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.7|1.7|CD|_
Paired-end|paired-end|NN|_ reads|read|VBZ|_ were|be|VBD|_ merged|merge|VBN|_ to|to|TO|_ single|single|JJ|_ end|end|NN|_ fasta|fasta|NN|_ reads|read|VBZ|_ by|by|IN|_ usin|usin|NN|_ FlASh|flash|NN|_ software|software|NN|_ v1|v1|NN|_ .2.11|.2.11|CD|_
Labled|Labled|NNP|_ transcript|transcript|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ merged|merged|JJ|_ single|single|JJ|_ end|end|NN|_ reads|read|VBZ|_ and|and|CC|_ processed|process|VBN|_ to|to|TO|_ paired-end|paired-end|JJ|_ reads|read|VBZ|_ again|again|RB|_ by|by|IN|_ custom|custom|NN|_ program|program|NN|_ scripts|script|NNS|_
Extracted|extract|VBN|_ paired-end|paired-end|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ E.coli|e.coli|JJ|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 00913.3|00913.3|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ v2|v2|NN|_ .3.4.1|.3.4.1|CD|_ ,|,|,|_ and|and|CC|_ single|single|JJ|_ end|end|NN|_ full|full|JJ|_ length|length|NN|_ sequence|sequence|NN|_ was|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ the|the|DT|_ paried-end|paried-end|JJ|_ data|datum|NNS|_ by|by|IN|_ custome|custome|NN|_ transcripts|transcript|NNS|_ and|and|CC|_ Bowtie2|bowtie2|NN|_ .|.|.|_
rRNA|rrna|NN|_ transcripts|transcript|NNS|_ were|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ TSSs|tsss|NNS|_ ,|,|,|_ TTSs|ttss|NNS|_ and|and|CC|_ overlap|overlap|VBP|_ TTSs|ttss|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ remaining|remain|VBG|_ data|datum|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|MG1655|NNP|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wig|wig|NN|_ files|file|NNS|_
For|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ samples|sample|NNS|_ ,|,|,|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 0.5|0.5|CD|_ volume|volume|NN|_ of|of|IN|_ cold|cold|JJ|_ Stop|stop|NN|_ Buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ immediately|immediately|RB|_ to|to|TO|_ the|the|DT|_ culture|culture|NN|_ medium|medium|NN|_ before|before|IN|_ harvest|harvest|NN|_ and|and|CC|_ stay|stay|VB|_ on|on|IN|_ the|the|DT|_ ice|ice|NN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 6,000|6,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ thoroughly|thoroughly|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ μl|μl|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ solution|solution|NN|_ -LSB-|-lsb-|-LRB-|_ 2|2|CD|_ mg/ml|mg/ml|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 2|2|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TRIzol|trizol|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ 15596|15596|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ following|follow|VBG|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ ChIP-seq|ChIP-seq|NNP|_ samples|sample|NNS|_ ,|,|,|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ with|with|IN|_ continued|continued|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ before|before|IN|_ quenching|quench|VBG|_ with|with|IN|_ glycine|glycine|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ lysed|lyse|VBN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ sheared|shear|VBN|_ by|by|IN|_ sonication|sonication|NN|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ and|and|CC|_ RNase|rnase|NN|_ A.|a.|NN|_ Antibody|antibody|NN|_ against|against|IN|_ RNAP|rnap|NN|_ β|β|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ target|target|NN|_ DNA|dna|NN|_ enrichment|enrichment|NN|_ .|.|.|_
A|a|DT|_ new|new|JJ|_ RNA-seq|rna-seq|NN|_ method|method|NN|_ SEnd-seq|send-seq|NN|_ was|be|VBD|_ developed|develop|VBN|_ and|and|CC|_ used|use|VBN|_ to|to|TO|_ prepare|prepare|VB|_ the|the|DT|_ SEnd-seq|send-seq|JJ|_ library|library|NN|_ ,|,|,|_ standard|standard|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ RS-122-2101|rs-122-2101|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ ChIP-seq|ChIP-seq|NNP|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ II|ii|CD|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ ,|,|,|_ E7645|e7645|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ ChIP|chip|NN|_ DNA|dna|NN|_ enrichment|enrichment|NN|_ .|.|.|_ For|for|IN|_ SEnd|send|VB|_ _|_|SYM|_ seq|seq|NN|_ ,|,|,|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ RNA|rna|NN|_ adaptor|adaptor|NN|_ -LRB-|-lrb-|-LRB-|_ /|/|:|_ 5Phos/rNrNrN|5phos/rnrnrn|NN|_ rNrArArCrCrUrGrCrUrArUrCrArArCrUrG/3ddC|rnrararcrcrurgrcrurarurcrararcrurg/3ddc|NN|_ /|/|:|_ or|or|CC|_ /|/|:|_ 5Phos/rNrNrN|5phos/rnrnrn|NN|_ rNrGrCrUrUrCrCrUrGrCrUrArUrCrArArCrUrG/3ddC|rnrgrcrururcrcrurgrcrurarurcrararcrurg/3ddc|NN|_ /|/|:|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ both|both|DT|_ adaptors|adaptor|NNS|_ were|be|VBD|_ used|use|VBN|_ if|if|IN|_ two|two|CD|_ different|different|JJ|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ together|together|RB|_ for|for|IN|_ library|library|NN|_ preparation|preparation|NN|_ -LRB-|-lrb-|-LRB-|_ Log|log|NN|_ phase|phase|NN|_ samples|sample|NNS|_ used|use|VBD|_ the|the|DT|_ first|first|JJ|_ one|one|CD|_ and|and|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase samples|sample|NNS|_ used|use|VBD|_ the|the|DT|_ second|second|JJ|_ one|one|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ ligated|ligate|VBN|_ RNA|rna|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ cDNA|cdna|NN|_ with|with|IN|_ the|the|DT|_ same|same|JJ|_ Biotinylated|biotinylate|VBN|_ RT|rt|NN|_ primer|primer|NN|_ -LRB-|-lrb-|-LRB-|_ 5GGGCAG|5gggcag|NN|_ T/iBiodT/GATAGCAGG|t/ibiodt/gatagcagg|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ rRNA|rrna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ For|for|IN|_ ChIP-seq|ChIP-seq|NNP|_ ,|,|,|_ the|the|DT|_ enriched|enriched|JJ|_ ChIP|chip|NN|_ DNA|dna|NN|_ and|and|CC|_ input|input|NN|_ DNA|dna|NN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ II|ii|CD|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 10|10|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.4|7.4|CD|_ -RRB-|-rrb-|-RRB-|_ under|under|IN|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ temperature-sensitive|temperature-sensitive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ mutant|mutant|JJ|_ E.coli|e.coli|NN|_ strain|strain|NN|_ -LSB-|-lsb-|-LRB-|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ for|for|IN|_ normal|normal|JJ|_ culture|culture|NN|_ and|and|CC|_ shift|shift|NN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ to|to|TO|_ deactive|deactive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|JJ|_ cell|cell|NN|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ pnp|pnp|NN|GEN knoctout|knoctout|NN|_ ,|,|,|_ rnb|rnb|NN|GEN knoctout|knoctout|NN|_ and|and|CC|_ rnr|rnr|NN|GEN knoct|knoct|NN|_ out|out|IN|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ and|and|CC|_ ChIP-seq|chip-seq|JJ|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ when|when|WRB|_ the|the|DT|_ growth|growth|NN|_ stage|stage|NN|_ of|of|IN|_ indicated|indicate|VBN|_ cells|cell|NNS|_ reached|reach|VBD|_ to|to|TO|_ log|log|VB|_ phase|phase|NN|_ or|or|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ mutation|mutation|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ or|or|CC|_ shifted|shift|VBN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ in|in|IN|_ water|water|NN|_ bath|bath|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ to|to|TO|_ deactivate|deactivate|VB|_ RNase|rnase|NN|_ E|e|NN|_ .|.|.|_ In|in|IN|_ order|order|NN|_ to|to|TO|_ inactive|inactive|JJ|_ the|the|DT|_ rho|rho|NN|GEN activity|activity|NN|_ ,|,|,|_ the|the|DT|_ wild|wild|JJ|_ type|type|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ 50|50|CD|_ μg/ml|μg/ml|NN|_ bicyclomycin|bicyclomycin|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ at|at|IN|_ indicated|indicated|JJ|_ growth|growth|NN|_ condition|condition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_
treatment|treatment|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_
strain|strain|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 10|10|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.4|7.4|CD|_ -RRB-|-rrb-|-RRB-|_ under|under|IN|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ temperature-sensitive|temperature-sensitive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ mutant|mutant|JJ|_ E.coli|e.coli|NN|_ strain|strain|NN|_ -LSB-|-lsb-|-LRB-|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ for|for|IN|_ normal|normal|JJ|_ culture|culture|NN|_ and|and|CC|_ shift|shift|NN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ to|to|TO|_ deactive|deactive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|JJ|_ cell|cell|NN|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ pnp|pnp|NN|GEN knoctout|knoctout|NN|_ ,|,|,|_ rnb|rnb|NN|GEN knoctout|knoctout|NN|_ and|and|CC|_ rnr|rnr|NN|GEN knoct|knoct|NN|_ out|out|IN|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ and|and|CC|_ ChIP-seq|chip-seq|JJ|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ when|when|WRB|_ the|the|DT|_ growth|growth|NN|_ stage|stage|NN|_ of|of|IN|_ indicated|indicate|VBN|_ cells|cell|NNS|_ reached|reach|VBD|_ to|to|TO|_ log|log|VB|_ phase|phase|NN|_ or|or|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ mutation|mutation|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ or|or|CC|_ shifted|shift|VBN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ in|in|IN|_ water|water|NN|_ bath|bath|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ to|to|TO|_ deactivate|deactivate|VB|_ RNase|rnase|NN|_ E|e|NN|_ .|.|.|_ In|in|IN|_ order|order|NN|_ to|to|TO|_ inactive|inactive|JJ|_ the|the|DT|_ rho|rho|NN|GEN activity|activity|NN|_ ,|,|,|_ the|the|DT|_ wild|wild|JJ|_ type|type|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ 50|50|CD|_ μg/ml|μg/ml|NN|_ bicyclomycin|bicyclomycin|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ at|at|IN|_ indicated|indicated|JJ|_ growth|growth|NN|_ condition|condition|NN|_ .|.|.|_
Xiangwu|xiangwu|NN|_ ,|,|,|_ ,|,|,|_ Ju|ju|NN|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.7|1.7|CD|_
Paired-end|paired-end|NN|_ reads|read|VBZ|_ were|be|VBD|_ merged|merge|VBN|_ to|to|TO|_ single|single|JJ|_ end|end|NN|_ fasta|fasta|NN|_ reads|read|VBZ|_ by|by|IN|_ usin|usin|NN|_ FlASh|flash|NN|_ software|software|NN|_ v1|v1|NN|_ .2.11|.2.11|CD|_
Labled|Labled|NNP|_ transcript|transcript|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ merged|merged|JJ|_ single|single|JJ|_ end|end|NN|_ reads|read|VBZ|_ and|and|CC|_ processed|process|VBN|_ to|to|TO|_ paired-end|paired-end|JJ|_ reads|read|VBZ|_ again|again|RB|_ by|by|IN|_ custom|custom|NN|_ program|program|NN|_ scripts|script|NNS|_
Extracted|extract|VBN|_ paired-end|paired-end|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ E.coli|e.coli|JJ|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 00913.3|00913.3|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ v2|v2|NN|_ .3.4.1|.3.4.1|CD|_ ,|,|,|_ and|and|CC|_ single|single|JJ|_ end|end|NN|_ full|full|JJ|_ length|length|NN|_ sequence|sequence|NN|_ was|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ the|the|DT|_ paried-end|paried-end|JJ|_ data|datum|NNS|_ by|by|IN|_ custome|custome|NN|_ transcripts|transcript|NNS|_ and|and|CC|_ Bowtie2|bowtie2|NN|_ .|.|.|_
rRNA|rrna|NN|_ transcripts|transcript|NNS|_ were|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ TSSs|tsss|NNS|_ ,|,|,|_ TTSs|ttss|NNS|_ and|and|CC|_ overlap|overlap|VBP|_ TTSs|ttss|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ remaining|remain|VBG|_ data|datum|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|MG1655|NNP|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wig|wig|NN|_ files|file|NNS|_
For|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ samples|sample|NNS|_ ,|,|,|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 0.5|0.5|CD|_ volume|volume|NN|_ of|of|IN|_ cold|cold|JJ|_ Stop|stop|NN|_ Buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ immediately|immediately|RB|_ to|to|TO|_ the|the|DT|_ culture|culture|NN|_ medium|medium|NN|_ before|before|IN|_ harvest|harvest|NN|_ and|and|CC|_ stay|stay|VB|_ on|on|IN|_ the|the|DT|_ ice|ice|NN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 6,000|6,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ thoroughly|thoroughly|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ μl|μl|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ solution|solution|NN|_ -LSB-|-lsb-|-LRB-|_ 2|2|CD|_ mg/ml|mg/ml|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 2|2|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TRIzol|trizol|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ 15596|15596|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ following|follow|VBG|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ ChIP-seq|ChIP-seq|NNP|_ samples|sample|NNS|_ ,|,|,|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ with|with|IN|_ continued|continued|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ before|before|IN|_ quenching|quench|VBG|_ with|with|IN|_ glycine|glycine|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ lysed|lyse|VBN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ sheared|shear|VBN|_ by|by|IN|_ sonication|sonication|NN|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ and|and|CC|_ RNase|rnase|NN|_ A.|a.|NN|_ Antibody|antibody|NN|_ against|against|IN|_ RNAP|rnap|NN|_ β|β|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ target|target|NN|_ DNA|dna|NN|_ enrichment|enrichment|NN|_ .|.|.|_
A|a|DT|_ new|new|JJ|_ RNA-seq|rna-seq|NN|_ method|method|NN|_ SEnd-seq|send-seq|NN|_ was|be|VBD|_ developed|develop|VBN|_ and|and|CC|_ used|use|VBN|_ to|to|TO|_ prepare|prepare|VB|_ the|the|DT|_ SEnd-seq|send-seq|JJ|_ library|library|NN|_ ,|,|,|_ standard|standard|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ RS-122-2101|rs-122-2101|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ ChIP-seq|ChIP-seq|NNP|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ II|ii|CD|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ ,|,|,|_ E7645|e7645|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ ChIP|chip|NN|_ DNA|dna|NN|_ enrichment|enrichment|NN|_ .|.|.|_ For|for|IN|_ SEnd|send|VB|_ _|_|SYM|_ seq|seq|NN|_ ,|,|,|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ RNA|rna|NN|_ adaptor|adaptor|NN|_ -LRB-|-lrb-|-LRB-|_ /|/|:|_ 5Phos/rNrNrN|5phos/rnrnrn|NN|_ rNrArArCrCrUrGrCrUrArUrCrArArCrUrG/3ddC|rnrararcrcrurgrcrurarurcrararcrurg/3ddc|NN|_ /|/|:|_ or|or|CC|_ /|/|:|_ 5Phos/rNrNrN|5phos/rnrnrn|NN|_ rNrGrCrUrUrCrCrUrGrCrUrArUrCrArArCrUrG/3ddC|rnrgrcrururcrcrurgrcrurarurcrararcrurg/3ddc|NN|_ /|/|:|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ both|both|DT|_ adaptors|adaptor|NNS|_ were|be|VBD|_ used|use|VBN|_ if|if|IN|_ two|two|CD|_ different|different|JJ|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ together|together|RB|_ for|for|IN|_ library|library|NN|_ preparation|preparation|NN|_ -LRB-|-lrb-|-LRB-|_ Log|log|NN|_ phase|phase|NN|_ samples|sample|NNS|_ used|use|VBD|_ the|the|DT|_ first|first|JJ|_ one|one|CD|_ and|and|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase samples|sample|NNS|_ used|use|VBD|_ the|the|DT|_ second|second|JJ|_ one|one|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ ligated|ligate|VBN|_ RNA|rna|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ cDNA|cdna|NN|_ with|with|IN|_ the|the|DT|_ same|same|JJ|_ Biotinylated|biotinylate|VBN|_ RT|rt|NN|_ primer|primer|NN|_ -LRB-|-lrb-|-LRB-|_ 5GGGCAG|5gggcag|NN|_ T/iBiodT/GATAGCAGG|t/ibiodt/gatagcagg|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ rRNA|rrna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ For|for|IN|_ ChIP-seq|ChIP-seq|NNP|_ ,|,|,|_ the|the|DT|_ enriched|enriched|JJ|_ ChIP|chip|NN|_ DNA|dna|NN|_ and|and|CC|_ input|input|NN|_ DNA|dna|NN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ II|ii|CD|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 10|10|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.4|7.4|CD|_ -RRB-|-rrb-|-RRB-|_ under|under|IN|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ temperature-sensitive|temperature-sensitive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ mutant|mutant|JJ|_ E.coli|e.coli|NN|_ strain|strain|NN|_ -LSB-|-lsb-|-LRB-|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ for|for|IN|_ normal|normal|JJ|_ culture|culture|NN|_ and|and|CC|_ shift|shift|NN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ to|to|TO|_ deactive|deactive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|JJ|_ cell|cell|NN|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ pnp|pnp|NN|GEN knoctout|knoctout|NN|_ ,|,|,|_ rnb|rnb|NN|GEN knoctout|knoctout|NN|_ and|and|CC|_ rnr|rnr|NN|GEN knoct|knoct|NN|_ out|out|IN|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ and|and|CC|_ ChIP-seq|chip-seq|JJ|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ when|when|WRB|_ the|the|DT|_ growth|growth|NN|_ stage|stage|NN|_ of|of|IN|_ indicated|indicate|VBN|_ cells|cell|NNS|_ reached|reach|VBD|_ to|to|TO|_ log|log|VB|_ phase|phase|NN|_ or|or|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ mutation|mutation|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ or|or|CC|_ shifted|shift|VBN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ in|in|IN|_ water|water|NN|_ bath|bath|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ to|to|TO|_ deactivate|deactivate|VB|_ RNase|rnase|NN|_ E|e|NN|_ .|.|.|_ In|in|IN|_ order|order|NN|_ to|to|TO|_ inactive|inactive|JJ|_ the|the|DT|_ rho|rho|NN|GEN activity|activity|NN|_ ,|,|,|_ the|the|DT|_ wild|wild|JJ|_ type|type|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ 50|50|CD|_ μg/ml|μg/ml|NN|_ bicyclomycin|bicyclomycin|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ at|at|IN|_ indicated|indicated|JJ|_ growth|growth|NN|_ condition|condition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_
treatment|treatment|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_
strain|strain|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 10|10|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.4|7.4|CD|_ -RRB-|-rrb-|-RRB-|_ under|under|IN|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ temperature-sensitive|temperature-sensitive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ mutant|mutant|JJ|_ E.coli|e.coli|NN|_ strain|strain|NN|_ -LSB-|-lsb-|-LRB-|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ for|for|IN|_ normal|normal|JJ|_ culture|culture|NN|_ and|and|CC|_ shift|shift|NN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ to|to|TO|_ deactive|deactive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|JJ|_ cell|cell|NN|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ pnp|pnp|NN|GEN knoctout|knoctout|NN|_ ,|,|,|_ rnb|rnb|NN|GEN knoctout|knoctout|NN|_ and|and|CC|_ rnr|rnr|NN|GEN knoct|knoct|NN|_ out|out|IN|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ and|and|CC|_ ChIP-seq|chip-seq|JJ|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ when|when|WRB|_ the|the|DT|_ growth|growth|NN|_ stage|stage|NN|_ of|of|IN|_ indicated|indicate|VBN|_ cells|cell|NNS|_ reached|reach|VBD|_ to|to|TO|_ log|log|VB|_ phase|phase|NN|_ or|or|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ mutation|mutation|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ or|or|CC|_ shifted|shift|VBN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ in|in|IN|_ water|water|NN|_ bath|bath|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ to|to|TO|_ deactivate|deactivate|VB|_ RNase|rnase|NN|_ E|e|NN|_ .|.|.|_ In|in|IN|_ order|order|NN|_ to|to|TO|_ inactive|inactive|JJ|_ the|the|DT|_ rho|rho|NN|GEN activity|activity|NN|_ ,|,|,|_ the|the|DT|_ wild|wild|JJ|_ type|type|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ 50|50|CD|_ μg/ml|μg/ml|NN|_ bicyclomycin|bicyclomycin|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ at|at|IN|_ indicated|indicated|JJ|_ growth|growth|NN|_ condition|condition|NN|_ .|.|.|_
Xiangwu|xiangwu|NN|_ ,|,|,|_ ,|,|,|_ Ju|ju|NN|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.7|1.7|CD|_
Paired-end|paired-end|NN|_ reads|read|VBZ|_ were|be|VBD|_ merged|merge|VBN|_ to|to|TO|_ single|single|JJ|_ end|end|NN|_ fasta|fasta|NN|_ reads|read|VBZ|_ by|by|IN|_ usin|usin|NN|_ FlASh|flash|NN|_ software|software|NN|_ v1|v1|NN|_ .2.11|.2.11|CD|_
Labled|Labled|NNP|_ transcript|transcript|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ merged|merged|JJ|_ single|single|JJ|_ end|end|NN|_ reads|read|VBZ|_ and|and|CC|_ processed|process|VBN|_ to|to|TO|_ paired-end|paired-end|JJ|_ reads|read|VBZ|_ again|again|RB|_ by|by|IN|_ custom|custom|NN|_ program|program|NN|_ scripts|script|NNS|_
Extracted|extract|VBN|_ paired-end|paired-end|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ E.coli|e.coli|JJ|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 00913.3|00913.3|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ v2|v2|NN|_ .3.4.1|.3.4.1|CD|_ ,|,|,|_ and|and|CC|_ single|single|JJ|_ end|end|NN|_ full|full|JJ|_ length|length|NN|_ sequence|sequence|NN|_ was|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ the|the|DT|_ paried-end|paried-end|JJ|_ data|datum|NNS|_ by|by|IN|_ custome|custome|NN|_ transcripts|transcript|NNS|_ and|and|CC|_ Bowtie2|bowtie2|NN|_ .|.|.|_
rRNA|rrna|NN|_ transcripts|transcript|NNS|_ were|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ TSSs|tsss|NNS|_ ,|,|,|_ TTSs|ttss|NNS|_ and|and|CC|_ overlap|overlap|VBP|_ TTSs|ttss|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ remaining|remain|VBG|_ data|datum|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|MG1655|NNP|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wig|wig|NN|_ files|file|NNS|_
For|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ samples|sample|NNS|_ ,|,|,|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 0.5|0.5|CD|_ volume|volume|NN|_ of|of|IN|_ cold|cold|JJ|_ Stop|stop|NN|_ Buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ immediately|immediately|RB|_ to|to|TO|_ the|the|DT|_ culture|culture|NN|_ medium|medium|NN|_ before|before|IN|_ harvest|harvest|NN|_ and|and|CC|_ stay|stay|VB|_ on|on|IN|_ the|the|DT|_ ice|ice|NN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 6,000|6,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ thoroughly|thoroughly|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ μl|μl|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ solution|solution|NN|_ -LSB-|-lsb-|-LRB-|_ 2|2|CD|_ mg/ml|mg/ml|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 2|2|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TRIzol|trizol|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ 15596|15596|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ following|follow|VBG|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ ChIP-seq|ChIP-seq|NNP|_ samples|sample|NNS|_ ,|,|,|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ with|with|IN|_ continued|continued|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ before|before|IN|_ quenching|quench|VBG|_ with|with|IN|_ glycine|glycine|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ lysed|lyse|VBN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ sheared|shear|VBN|_ by|by|IN|_ sonication|sonication|NN|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ and|and|CC|_ RNase|rnase|NN|_ A.|a.|NN|_ Antibody|antibody|NN|_ against|against|IN|_ RNAP|rnap|NN|_ β|β|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ target|target|NN|_ DNA|dna|NN|_ enrichment|enrichment|NN|_ .|.|.|_
A|a|DT|_ new|new|JJ|_ RNA-seq|rna-seq|NN|_ method|method|NN|_ SEnd-seq|send-seq|NN|_ was|be|VBD|_ developed|develop|VBN|_ and|and|CC|_ used|use|VBN|_ to|to|TO|_ prepare|prepare|VB|_ the|the|DT|_ SEnd-seq|send-seq|JJ|_ library|library|NN|_ ,|,|,|_ standard|standard|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ RS-122-2101|rs-122-2101|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ ChIP-seq|ChIP-seq|NNP|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ II|ii|CD|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ ,|,|,|_ E7645|e7645|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ ChIP|chip|NN|_ DNA|dna|NN|_ enrichment|enrichment|NN|_ .|.|.|_ For|for|IN|_ SEnd|send|VB|_ _|_|SYM|_ seq|seq|NN|_ ,|,|,|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ RNA|rna|NN|_ adaptor|adaptor|NN|_ -LRB-|-lrb-|-LRB-|_ /|/|:|_ 5Phos/rNrNrN|5phos/rnrnrn|NN|_ rNrArArCrCrUrGrCrUrArUrCrArArCrUrG/3ddC|rnrararcrcrurgrcrurarurcrararcrurg/3ddc|NN|_ /|/|:|_ or|or|CC|_ /|/|:|_ 5Phos/rNrNrN|5phos/rnrnrn|NN|_ rNrGrCrUrUrCrCrUrGrCrUrArUrCrArArCrUrG/3ddC|rnrgrcrururcrcrurgrcrurarurcrararcrurg/3ddc|NN|_ /|/|:|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ both|both|DT|_ adaptors|adaptor|NNS|_ were|be|VBD|_ used|use|VBN|_ if|if|IN|_ two|two|CD|_ different|different|JJ|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ together|together|RB|_ for|for|IN|_ library|library|NN|_ preparation|preparation|NN|_ -LRB-|-lrb-|-LRB-|_ Log|log|NN|_ phase|phase|NN|_ samples|sample|NNS|_ used|use|VBD|_ the|the|DT|_ first|first|JJ|_ one|one|CD|_ and|and|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase samples|sample|NNS|_ used|use|VBD|_ the|the|DT|_ second|second|JJ|_ one|one|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ ligated|ligate|VBN|_ RNA|rna|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ cDNA|cdna|NN|_ with|with|IN|_ the|the|DT|_ same|same|JJ|_ Biotinylated|biotinylate|VBN|_ RT|rt|NN|_ primer|primer|NN|_ -LRB-|-lrb-|-LRB-|_ 5GGGCAG|5gggcag|NN|_ T/iBiodT/GATAGCAGG|t/ibiodt/gatagcagg|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ rRNA|rrna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ For|for|IN|_ ChIP-seq|ChIP-seq|NNP|_ ,|,|,|_ the|the|DT|_ enriched|enriched|JJ|_ ChIP|chip|NN|_ DNA|dna|NN|_ and|and|CC|_ input|input|NN|_ DNA|dna|NN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ II|ii|CD|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 10|10|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.4|7.4|CD|_ -RRB-|-rrb-|-RRB-|_ under|under|IN|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ temperature-sensitive|temperature-sensitive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ mutant|mutant|JJ|_ E.coli|e.coli|NN|_ strain|strain|NN|_ -LSB-|-lsb-|-LRB-|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ for|for|IN|_ normal|normal|JJ|_ culture|culture|NN|_ and|and|CC|_ shift|shift|NN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ to|to|TO|_ deactive|deactive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|JJ|_ cell|cell|NN|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ pnp|pnp|NN|GEN knoctout|knoctout|NN|_ ,|,|,|_ rnb|rnb|NN|GEN knoctout|knoctout|NN|_ and|and|CC|_ rnr|rnr|NN|GEN knoct|knoct|NN|_ out|out|IN|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ and|and|CC|_ ChIP-seq|chip-seq|JJ|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ when|when|WRB|_ the|the|DT|_ growth|growth|NN|_ stage|stage|NN|_ of|of|IN|_ indicated|indicate|VBN|_ cells|cell|NNS|_ reached|reach|VBD|_ to|to|TO|_ log|log|VB|_ phase|phase|NN|_ or|or|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ mutation|mutation|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ or|or|CC|_ shifted|shift|VBN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ in|in|IN|_ water|water|NN|_ bath|bath|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ to|to|TO|_ deactivate|deactivate|VB|_ RNase|rnase|NN|_ E|e|NN|_ .|.|.|_ In|in|IN|_ order|order|NN|_ to|to|TO|_ inactive|inactive|JJ|_ the|the|DT|_ rho|rho|NN|GEN activity|activity|NN|_ ,|,|,|_ the|the|DT|_ wild|wild|JJ|_ type|type|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ 50|50|CD|_ μg/ml|μg/ml|NN|_ bicyclomycin|bicyclomycin|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ at|at|IN|_ indicated|indicated|JJ|_ growth|growth|NN|_ condition|condition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ Stationary|stationary|JJ|_ phase|phase|NN|_
treatment|treatment|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_
strain|strain|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 10|10|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.4|7.4|CD|_ -RRB-|-rrb-|-RRB-|_ under|under|IN|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ temperature-sensitive|temperature-sensitive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ mutant|mutant|JJ|_ E.coli|e.coli|NN|_ strain|strain|NN|_ -LSB-|-lsb-|-LRB-|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ for|for|IN|_ normal|normal|JJ|_ culture|culture|NN|_ and|and|CC|_ shift|shift|NN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ to|to|TO|_ deactive|deactive|JJ|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|JJ|_ cell|cell|NN|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ pnp|pnp|NN|GEN knoctout|knoctout|NN|_ ,|,|,|_ rnb|rnb|NN|GEN knoctout|knoctout|NN|_ and|and|CC|_ rnr|rnr|NN|GEN knoct|knoct|NN|_ out|out|IN|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ and|and|CC|_ ChIP-seq|chip-seq|JJ|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ when|when|WRB|_ the|the|DT|_ growth|growth|NN|_ stage|stage|NN|_ of|of|IN|_ indicated|indicate|VBN|_ cells|cell|NNS|_ reached|reach|VBD|_ to|to|TO|_ log|log|VB|_ phase|phase|NN|_ or|or|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_ mutation|mutation|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 28|28|CD|_ °C|°c|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ RNase|rnase|NN|_ E|e|NN|_ activity|activity|NN|_ or|or|CC|_ shifted|shift|VBN|_ to|to|TO|_ 44|44|CD|_ °C|°c|NN|_ in|in|IN|_ water|water|NN|_ bath|bath|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ to|to|TO|_ deactivate|deactivate|VB|_ RNase|rnase|NN|_ E|e|NN|_ .|.|.|_ In|in|IN|_ order|order|NN|_ to|to|TO|_ inactive|inactive|JJ|_ the|the|DT|_ rho|rho|NN|GEN activity|activity|NN|_ ,|,|,|_ the|the|DT|_ wild|wild|JJ|_ type|type|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ 50|50|CD|_ μg/ml|μg/ml|NN|_ bicyclomycin|bicyclomycin|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ at|at|IN|_ indicated|indicated|JJ|_ growth|growth|NN|_ condition|condition|NN|_ .|.|.|_
Xiangwu|xiangwu|NN|_ ,|,|,|_ ,|,|,|_ Ju|Ju|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10mM|10mm|NN|_ glutamate|glutamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ media|media|NNS|_ MG|mg|NN|_ _|_|SYM|_ glu|glu|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|NN|_ glu|glu|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP w/o|w/o|NN|_ trace|trace|NN|_ elements|element|NNS|_
knock-out|knock-out|NN|_ :|:|:|_ --|--|:|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10mM|10mm|NN|_ glutamate|glutamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ media|media|NNS|_ MG|mg|NN|_ _|_|SYM|_ glu|glu|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|NN|_ glu|glu|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10mM|10mm|NN|_ glutamate|glutamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ media|media|NNS|_ MG|mg|NN|_ _|_|SYM|_ glu|glu|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|NN|_ glu|glu|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP w/o|w/o|NN|_ trace|trace|NN|_ elements|element|NNS|_
knock-out|knock-out|NN|_ :|:|:|_ --|--|:|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10mM|10mm|NN|_ glutamate|glutamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ media|media|NNS|_ MG|mg|NN|_ _|_|SYM|_ glu|glu|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|NN|_ glu|glu|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10mM|10mm|NN|_ glutamate|glutamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ media|media|NNS|_ MG|mg|NN|_ _|_|SYM|_ glu|glu|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|NN|_ glu|glu|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 10mM|10mm|NN|_ glutamate|glutamate|JJ|_
knock-out|knock-out|NN|_ :|:|:|_ --|--|:|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10mM|10mm|NN|_ glutamate|glutamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ media|media|NNS|_ MG|mg|NN|_ _|_|SYM|_ glu|glu|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|NN|_ glu|glu|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10mM|10mm|NN|_ glutamate|glutamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ media|media|NNS|_ MG|mg|NN|_ _|_|SYM|_ glu|glu|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|NN|_ glu|glu|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 10mM|10mm|NN|_ glutamate|glutamate|JJ|_
knock-out|knock-out|NN|_ :|:|:|_ --|--|:|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10mM|10mm|NN|_ glutamate|glutamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ media|media|NNS|_ MG|mg|NN|_ _|_|SYM|_ glu|glu|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|NN|_ glu|glu|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10mM|10mm|NN|_ glutamate|glutamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ media|media|NNS|_ MG|mg|NN|_ _|_|SYM|_ glu|glu|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|NN|_ glu|glu|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
knock-out|knock-out|NN|_ :|:|:|_ --|--|:|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED was|be|VBD|_ also|also|RB|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|CD|_ no|no|DT|_ _|_|NN|_ te|te|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10mM|10mm|NN|_ glutamate|glutamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ media|media|NNS|_ MG|mg|NN|_ _|_|SYM|_ glu|glu|FW|_ _|_|FW|_ 1|1|CD|_ and|and|CC|_ MG|mg|NN|_ _|_|NN|_ glu|glu|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ D-sorbitol|d-sorbitol|NN|_
supplement|supplement|NN|_ :|:|:|_ L-arginine|l-arginine|NN|_ -LRB-|-lrb-|-LRB-|_ 5.75|5.75|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ D-sorbitol|d-sorbitol|NN|_
supplement|supplement|NN|_ :|:|:|_ L-arginine|l-arginine|NN|_ -LRB-|-lrb-|-LRB-|_ 5.75|5.75|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ D-ribose|d-ribose|NN|_
supplement|supplement|NN|_ :|:|:|_ Cytidine|cytidine|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ D-ribose|d-ribose|NN|_
supplement|supplement|NN|_ :|:|:|_ Cytidine|cytidine|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
supplement|supplement|NN|_ :|:|:|_ glutathione|glutathione|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
supplement|supplement|NN|_ :|:|:|_ glutathione|glutathione|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucarate|glucarate|NN|_
supplement|supplement|NN|_ :|:|:|_ leucine|leucine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10mM|10mm|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucarate|glucarate|NN|_
supplement|supplement|NN|_ :|:|:|_ leucine|leucine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10mM|10mm|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
supplement|supplement|NN|_ :|:|:|_ methionine|methionine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 5mM|5mm|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
supplement|supplement|NN|_ :|:|:|_ methionine|methionine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 5mM|5mm|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
supplement|supplement|NN|_ :|:|:|_ KNO3|kno3|NN|_ -LRB-|-lrb-|-LRB-|_ 20mM|20mm|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
supplement|supplement|NN|_ :|:|:|_ KNO3|kno3|NN|_ -LRB-|-lrb-|-LRB-|_ 20mM|20mm|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ N-acetylglucosamine|n-acetylglucosamine|NN|_
supplement|supplement|NN|_ :|:|:|_ phenylalanine|phenylalanine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 5mM|5mm|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ N-acetylglucosamine|n-acetylglucosamine|NN|_
supplement|supplement|NN|_ :|:|:|_ phenylalanine|phenylalanine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 5mM|5mm|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ galactose|galactose|NN|_
supplement|supplement|NN|_ :|:|:|_ thiamine|thiamine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 1uM|1um|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ galactose|galactose|NN|_
supplement|supplement|NN|_ :|:|:|_ thiamine|thiamine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 1uM|1um|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ D-gluconate|d-gluconate|JJ|_
supplement|supplement|NN|_ :|:|:|_ tyrosine|tyrosine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 5mM|5mm|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ D-gluconate|d-gluconate|JJ|_
supplement|supplement|NN|_ :|:|:|_ tyrosine|tyrosine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 5mM|5mm|NN|_ -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 3.3|3.3|CD|_ g/L|g/l|NN|_ pyruvate|pyruvate|NN|SUPP
supplement|supplement|NN|_ :|:|:|_ Uracil|Uracil|NNP|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 3.3|3.3|CD|_ g/L|g/l|NN|_ pyruvate|pyruvate|NN|SUPP
supplement|supplement|NN|_ :|:|:|_ Uracil|Uracil|NNP|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ BW25113|bw25113|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP cytidine|cytidine|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ BW25113|bw25113|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ BW25113|bw25113|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP cytidine|cytidine|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ BW25113|bw25113|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 100|100|CD|_ mg/L|mg/l|NN|_ adenine|adenine|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 100|100|CD|_ mg/L|mg/l|NN|_ adenine|adenine|NN|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ sample-specific|sample-specific|JJ|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ nitrate|nitrate|JJ|SUPP respiration|respiration|NN|_ cultures|culture|NNS|_ ,|,|,|_ a|a|DT|_ 35:50|35:50|CD|_ ratio|ratio|NN|_ of|of|IN|_ carbon|carbon|NN|_ dioxide|dioxide|NN|_ to|to|TO|_ nitrogen|nitrogen|NN|_ was|be|VBD|_ bubbled|bubble|VBN|_ through|through|IN|_ hte|hte|NN|_ media|media|NNS|_ to|to|TO|_ deoxygenate|deoxygenate|VB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genomes|genome|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_ .|.|.|_ Only|only|RB|_ 1100|1100|CD|_ genes|gene|NNS|_ common|common|JJ|_ across|across|IN|_ all|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ .|.|.|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genomes|genome|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .1.2|.1.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ mode|mode|NN|_ .|.|.|_ Only|only|RB|_ 1100|1100|CD|_ genes|gene|NNS|_ common|common|JJ|_ across|across|IN|_ all|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ .|.|.|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
After|after|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ growth|growth|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ Qiagen|Qiagen|NNP|_ RNA-protect|RNA-protect|NNP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 17,500|17,500|CD|_ RPMs|rpm|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ in|in|IN|_ the|the|DT|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ Readylyse|readylyse|NN|_ Lysozyme|lysozyme|NN|_ ,|,|,|_ SuperaseIn|superasein|NN|_ ,|,|,|_ Protease|protease|NN|_ K|k|NN|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ columns|column|NNS|_ and|and|CC|_ following|follow|VBG|_ vendor|vendor|NN|_ procedures|procedure|NNS|_ .|.|.|_ An|a|DT|_ on-column|on-column|JJ|_ DNase-treatment|dnase-treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nano|Nano|NNP|_ drop|drop|NN|_ and|and|CC|_ quality|quality|NN|_ assessed|assess|VBN|_ by|by|IN|_ running|run|VBG|_ an|a|DT|_ RNA-nano|rna-nano|JJ|_ chip|chip|NN|_ on|on|IN|_ a|a|DT|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_ The|the|DT|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ .|.|.|_ A|a|DT|_ KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ KK8401|kk8401|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ create|create|VB|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ with|with|IN|_ an|a|DT|_ average|average|JJ|_ insert|insert|NN|_ length|length|NN|_ of|of|IN|_ around|around|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP
glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ 2g/L|2g/l|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_
Anand|Anand|NNP|_ ,|,|,|_ ,|,|,|_ Sastry|Sastry|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ .2.6|.2.6|CD|_ .|.|.|_
Cufflinks|Cufflinks|NNPS|_ v2|v2|NN|_ .2.1|.2.1|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ DEGs|deg|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ identified|identify|VBN|_ using|use|VBG|_ Cuffdiff|Cuffdiff|NNP|_ v2|v2|NN|_ .2.1|.2.1|CD|_ program|program|NN|_ and|and|CC|_ expression|expression|NN|_ of|of|IN|_ gene|gene|NN|_ with|with|IN|_ adjusted|adjusted|JJ|_ P-value|p-value|JJ|_ <|<|JJR|_ 0.05|0.05|CD|_ and|and|CC|_ log2|log2|CD|_ fold|fold|JJ|_ change|change|NN|_ ≥|≥|SYM|_ +1.0|+1.0|CD|_ or|or|CC|_ ≤|≤|CD|_ -1|-1|CD|_ was|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ An|a|DT|_ excel|excel|VB|_ file|file|NN|_ ,|,|,|_ where|where|WRB|_ cuffdiff|cuffdiff|JJ|_ results|result|NNS|_ are|be|VBP|_ given|give|VBN|_ including|include|VBG|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Analytik|Analytik|NNP|_ Jena|Jena|NNP|_ RNA|rna|NN|_ Mini|Mini|NNP|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ guidelines|guideline|NNS|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ constructed|construct|VBN|_ ,|,|,|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ Δfis|Δfis|NNP|_ and|and|CC|_ Δhns|Δhns|NNP|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ and|and|CC|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ 15g/l|15g/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Where|where|WRB|_ needed|need|VBN|_ ,|,|,|_ kanamycin|kanamycin|NN|_ was|be|VBD|_ used|use|VBN|_ at|at|IN|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 50µg/ml|50µg/ml|NN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 40|40|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ str|str|NN|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
material|material|NN|_ type|type|NN|_ :|:|:|_ whole|whole|JJ|_ organism|organism|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-fis|delta-fis|JJ|_
phenotype|phenotype|NN|_ :|:|:|_ lack|lack|NN|_ Fis|fis|NN|TF protein|protein|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ Δfis|Δfis|NNP|_ and|and|CC|_ Δhns|Δhns|NNP|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ and|and|CC|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ 15g/l|15g/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Where|where|WRB|_ needed|need|VBN|_ ,|,|,|_ kanamycin|kanamycin|NN|_ was|be|VBD|_ used|use|VBN|_ at|at|IN|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 50µg/ml|50µg/ml|NN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 40|40|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
Payel|payel|NN|_ ,|,|,|_ ,|,|,|_ Ghosh|Ghosh|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ .2.6|.2.6|CD|_ .|.|.|_
Cufflinks|Cufflinks|NNPS|_ v2|v2|NN|_ .2.1|.2.1|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ DEGs|deg|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ identified|identify|VBN|_ using|use|VBG|_ Cuffdiff|Cuffdiff|NNP|_ v2|v2|NN|_ .2.1|.2.1|CD|_ program|program|NN|_ and|and|CC|_ expression|expression|NN|_ of|of|IN|_ gene|gene|NN|_ with|with|IN|_ adjusted|adjusted|JJ|_ P-value|p-value|JJ|_ <|<|JJR|_ 0.05|0.05|CD|_ and|and|CC|_ log2|log2|CD|_ fold|fold|JJ|_ change|change|NN|_ ≥|≥|SYM|_ +1.0|+1.0|CD|_ or|or|CC|_ ≤|≤|CD|_ -1|-1|CD|_ was|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ An|a|DT|_ excel|excel|VB|_ file|file|NN|_ ,|,|,|_ where|where|WRB|_ cuffdiff|cuffdiff|JJ|_ results|result|NNS|_ are|be|VBP|_ given|give|VBN|_ including|include|VBG|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Analytik|Analytik|NNP|_ Jena|Jena|NNP|_ RNA|rna|NN|_ Mini|Mini|NNP|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ guidelines|guideline|NNS|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ constructed|construct|VBN|_ ,|,|,|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ Δfis|Δfis|NNP|_ and|and|CC|_ Δhns|Δhns|NNP|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ and|and|CC|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ 15g/l|15g/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Where|where|WRB|_ needed|need|VBN|_ ,|,|,|_ kanamycin|kanamycin|NN|_ was|be|VBD|_ used|use|VBN|_ at|at|IN|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 50µg/ml|50µg/ml|NN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 40|40|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ str|str|NN|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
material|material|NN|_ type|type|NN|_ :|:|:|_ whole|whole|JJ|_ organism|organism|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-fis|delta-fis|JJ|_
phenotype|phenotype|NN|_ :|:|:|_ lack|lack|NN|_ Fis|fis|NN|TF protein|protein|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ Δfis|Δfis|NNP|_ and|and|CC|_ Δhns|Δhns|NNP|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ and|and|CC|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ 15g/l|15g/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Where|where|WRB|_ needed|need|VBN|_ ,|,|,|_ kanamycin|kanamycin|NN|_ was|be|VBD|_ used|use|VBN|_ at|at|IN|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 50µg/ml|50µg/ml|NN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 40|40|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
Payel|payel|NN|_ ,|,|,|_ ,|,|,|_ Ghosh|Ghosh|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ .2.6|.2.6|CD|_ .|.|.|_
Cufflinks|Cufflinks|NNPS|_ v2|v2|NN|_ .2.1|.2.1|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ DEGs|deg|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ identified|identify|VBN|_ using|use|VBG|_ Cuffdiff|Cuffdiff|NNP|_ v2|v2|NN|_ .2.1|.2.1|CD|_ program|program|NN|_ and|and|CC|_ expression|expression|NN|_ of|of|IN|_ gene|gene|NN|_ with|with|IN|_ adjusted|adjusted|JJ|_ P-value|p-value|JJ|_ <|<|JJR|_ 0.05|0.05|CD|_ and|and|CC|_ log2|log2|CD|_ fold|fold|JJ|_ change|change|NN|_ ≥|≥|SYM|_ +1.0|+1.0|CD|_ or|or|CC|_ ≤|≤|CD|_ -1|-1|CD|_ was|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ An|a|DT|_ excel|excel|VB|_ file|file|NN|_ ,|,|,|_ where|where|WRB|_ cuffdiff|cuffdiff|JJ|_ results|result|NNS|_ are|be|VBP|_ given|give|VBN|_ including|include|VBG|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Analytik|Analytik|NNP|_ Jena|Jena|NNP|_ RNA|rna|NN|_ Mini|Mini|NNP|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ guidelines|guideline|NNS|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ constructed|construct|VBN|_ ,|,|,|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ Δfis|Δfis|NNP|_ and|and|CC|_ Δhns|Δhns|NNP|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ and|and|CC|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ 15g/l|15g/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Where|where|WRB|_ needed|need|VBN|_ ,|,|,|_ kanamycin|kanamycin|NN|_ was|be|VBD|_ used|use|VBN|_ at|at|IN|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 50µg/ml|50µg/ml|NN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 40|40|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ str|str|NN|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
material|material|NN|_ type|type|NN|_ :|:|:|_ whole|whole|JJ|_ organism|organism|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-hns|delta-hn|NNS|_
phenotype|phenotype|NN|_ :|:|:|_ lack|lack|NN|_ H-NS|h-ns|NN|_ protein|protein|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ Δfis|Δfis|NNP|_ and|and|CC|_ Δhns|Δhns|NNP|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ and|and|CC|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ 15g/l|15g/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Where|where|WRB|_ needed|need|VBN|_ ,|,|,|_ kanamycin|kanamycin|NN|_ was|be|VBD|_ used|use|VBN|_ at|at|IN|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 50µg/ml|50µg/ml|NN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 40|40|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
Payel|payel|NN|_ ,|,|,|_ ,|,|,|_ Ghosh|Ghosh|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ .2.6|.2.6|CD|_ .|.|.|_
Cufflinks|Cufflinks|NNPS|_ v2|v2|NN|_ .2.1|.2.1|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ DEGs|deg|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ identified|identify|VBN|_ using|use|VBG|_ Cuffdiff|Cuffdiff|NNP|_ v2|v2|NN|_ .2.1|.2.1|CD|_ program|program|NN|_ and|and|CC|_ expression|expression|NN|_ of|of|IN|_ gene|gene|NN|_ with|with|IN|_ adjusted|adjusted|JJ|_ P-value|p-value|JJ|_ <|<|JJR|_ 0.05|0.05|CD|_ and|and|CC|_ log2|log2|CD|_ fold|fold|JJ|_ change|change|NN|_ ≥|≥|SYM|_ +1.0|+1.0|CD|_ or|or|CC|_ ≤|≤|CD|_ -1|-1|CD|_ was|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ An|a|DT|_ excel|excel|VB|_ file|file|NN|_ ,|,|,|_ where|where|WRB|_ cuffdiff|cuffdiff|JJ|_ results|result|NNS|_ are|be|VBP|_ given|give|VBN|_ including|include|VBG|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Analytik|Analytik|NNP|_ Jena|Jena|NNP|_ RNA|rna|NN|_ Mini|Mini|NNP|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ guidelines|guideline|NNS|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ constructed|construct|VBN|_ ,|,|,|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ Δfis|Δfis|NNP|_ and|and|CC|_ Δhns|Δhns|NNP|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ and|and|CC|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ 15g/l|15g/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Where|where|WRB|_ needed|need|VBN|_ ,|,|,|_ kanamycin|kanamycin|NN|_ was|be|VBD|_ used|use|VBN|_ at|at|IN|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 50µg/ml|50µg/ml|NN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 40|40|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ str|str|NN|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
material|material|NN|_ type|type|NN|_ :|:|:|_ whole|whole|JJ|_ organism|organism|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-hns|delta-hn|NNS|_
phenotype|phenotype|NN|_ :|:|:|_ lack|lack|NN|_ H-NS|h-ns|NN|_ protein|protein|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ Δfis|Δfis|NNP|_ and|and|CC|_ Δhns|Δhns|NNP|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ and|and|CC|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ 15g/l|15g/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Where|where|WRB|_ needed|need|VBN|_ ,|,|,|_ kanamycin|kanamycin|NN|_ was|be|VBD|_ used|use|VBN|_ at|at|IN|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 50µg/ml|50µg/ml|NN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 40|40|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
Payel|payel|NN|_ ,|,|,|_ ,|,|,|_ Ghosh|Ghosh|NNP|_
quality|quality|NN|_ trimming|trim|VBG|_ -LRB-|-lrb-|-LRB-|_ cut-off|cut-off|JJ|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ adapter|adapter|NN|_ removal|removal|NN|_ using|use|VBG|_ cutadapt|cutadapt|JJ|_ 1.15|1.15|CD|_
generattion|generattion|NN|_ of|of|IN|_ reverse|reverse|JJ|_ complement|complement|NN|_ reads|read|VBZ|_ using|use|VBG|_ FASTX|FASTX|NNP|_ 0.0.14|0.0.14|CD|_
poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ φO104|φo104|NN|_ and|and|CC|_ φPA8|φpa8|NN|_ genomes|genome|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ -LRB-|-lrb-|-LRB-|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ with|with|IN|_ the|the|DT|_ locations|location|NNS|_ of|of|IN|_ the|the|DT|_ annotation|annotation|NN|_ entries|entry|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ qunatification|qunatification|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ annotation|annotation|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ DESeq2|deseq2|NN|_ 1.16.1|1.16.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ φPA8|φpa8|NN|_ -LRB-|-lrb-|-LRB-|_ KP682374|kp682374|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ φO104|φo104|NN|_ -LRB-|-lrb-|-LRB-|_ 3256115|3256115|CD|_ to|to|TO|_ 3317011|3317011|CD|_ from|from|IN|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ of|of|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ data|datum|NNS|_ used|use|VBN|_ for|for|IN|_ DESeq2|deseq2|NN|_ analysis|analysis|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RiboLock|RiboLock|NNP|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ further|further|JJ|_ treated|treat|VBN|_ with|with|IN|_ RiboZero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ Qubit|qubit|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ naive|naive|JJ|_ -LRB-|-lrb-|-LRB-|_ wild|wild|JJ|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
Petya|petya|NN|_ ,|,|,|_ ,|,|,|_ Berger|Berger|NNP|_
quality|quality|NN|_ trimming|trim|VBG|_ -LRB-|-lrb-|-LRB-|_ cut-off|cut-off|JJ|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ adapter|adapter|NN|_ removal|removal|NN|_ using|use|VBG|_ cutadapt|cutadapt|JJ|_ 1.15|1.15|CD|_
generattion|generattion|NN|_ of|of|IN|_ reverse|reverse|JJ|_ complement|complement|NN|_ reads|read|VBZ|_ using|use|VBG|_ FASTX|FASTX|NNP|_ 0.0.14|0.0.14|CD|_
poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ φO104|φo104|NN|_ and|and|CC|_ φPA8|φpa8|NN|_ genomes|genome|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ -LRB-|-lrb-|-LRB-|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ with|with|IN|_ the|the|DT|_ locations|location|NNS|_ of|of|IN|_ the|the|DT|_ annotation|annotation|NN|_ entries|entry|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ qunatification|qunatification|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ annotation|annotation|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ DESeq2|deseq2|NN|_ 1.16.1|1.16.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ φPA8|φpa8|NN|_ -LRB-|-lrb-|-LRB-|_ KP682374|kp682374|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ φO104|φo104|NN|_ -LRB-|-lrb-|-LRB-|_ 3256115|3256115|CD|_ to|to|TO|_ 3317011|3317011|CD|_ from|from|IN|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ of|of|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ data|datum|NNS|_ used|use|VBN|_ for|for|IN|_ DESeq2|deseq2|NN|_ analysis|analysis|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RiboLock|RiboLock|NNP|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ further|further|JJ|_ treated|treat|VBN|_ with|with|IN|_ RiboZero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ Qubit|qubit|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ naive|naive|JJ|_ -LRB-|-lrb-|-LRB-|_ wild|wild|JJ|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
Petya|petya|NN|_ ,|,|,|_ ,|,|,|_ Berger|Berger|NNP|_
quality|quality|NN|_ trimming|trim|VBG|_ -LRB-|-lrb-|-LRB-|_ cut-off|cut-off|JJ|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ adapter|adapter|NN|_ removal|removal|NN|_ using|use|VBG|_ cutadapt|cutadapt|JJ|_ 1.15|1.15|CD|_
generattion|generattion|NN|_ of|of|IN|_ reverse|reverse|JJ|_ complement|complement|NN|_ reads|read|VBZ|_ using|use|VBG|_ FASTX|FASTX|NNP|_ 0.0.14|0.0.14|CD|_
poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ φO104|φo104|NN|_ and|and|CC|_ φPA8|φpa8|NN|_ genomes|genome|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ -LRB-|-lrb-|-LRB-|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ with|with|IN|_ the|the|DT|_ locations|location|NNS|_ of|of|IN|_ the|the|DT|_ annotation|annotation|NN|_ entries|entry|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ qunatification|qunatification|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ annotation|annotation|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ DESeq2|deseq2|NN|_ 1.16.1|1.16.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ φPA8|φpa8|NN|_ -LRB-|-lrb-|-LRB-|_ KP682374|kp682374|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ φO104|φo104|NN|_ -LRB-|-lrb-|-LRB-|_ 3256115|3256115|CD|_ to|to|TO|_ 3317011|3317011|CD|_ from|from|IN|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ of|of|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ data|datum|NNS|_ used|use|VBN|_ for|for|IN|_ DESeq2|deseq2|NN|_ analysis|analysis|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RiboLock|RiboLock|NNP|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ further|further|JJ|_ treated|treat|VBN|_ with|with|IN|_ RiboZero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ Qubit|qubit|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ naive|naive|JJ|_ -LRB-|-lrb-|-LRB-|_ wild|wild|JJ|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
Petya|petya|NN|_ ,|,|,|_ ,|,|,|_ Berger|Berger|NNP|_
quality|quality|NN|_ trimming|trim|VBG|_ -LRB-|-lrb-|-LRB-|_ cut-off|cut-off|JJ|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ adapter|adapter|NN|_ removal|removal|NN|_ using|use|VBG|_ cutadapt|cutadapt|JJ|_ 1.15|1.15|CD|_
generattion|generattion|NN|_ of|of|IN|_ reverse|reverse|JJ|_ complement|complement|NN|_ reads|read|VBZ|_ using|use|VBG|_ FASTX|FASTX|NNP|_ 0.0.14|0.0.14|CD|_
poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ φO104|φo104|NN|_ and|and|CC|_ φPA8|φpa8|NN|_ genomes|genome|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ -LRB-|-lrb-|-LRB-|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ with|with|IN|_ the|the|DT|_ locations|location|NNS|_ of|of|IN|_ the|the|DT|_ annotation|annotation|NN|_ entries|entry|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ qunatification|qunatification|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ annotation|annotation|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ DESeq2|deseq2|NN|_ 1.16.1|1.16.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ φPA8|φpa8|NN|_ -LRB-|-lrb-|-LRB-|_ KP682374|kp682374|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ φO104|φo104|NN|_ -LRB-|-lrb-|-LRB-|_ 3256115|3256115|CD|_ to|to|TO|_ 3317011|3317011|CD|_ from|from|IN|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ of|of|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ data|datum|NNS|_ used|use|VBN|_ for|for|IN|_ DESeq2|deseq2|NN|_ analysis|analysis|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RiboLock|RiboLock|NNP|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ further|further|JJ|_ treated|treat|VBN|_ with|with|IN|_ RiboZero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ Qubit|qubit|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ :|:|:|_ :|:|:|_ φO104|φo104|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ phageO104|phageo104|NN|_ in|in|IN|_ the|the|DT|_ wrbA|wrba|NN|GEN gene|gene|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ :|:|:|_ :|:|:|_ φO104|φo104|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
Petya|petya|NN|_ ,|,|,|_ ,|,|,|_ Berger|Berger|NNP|_
quality|quality|NN|_ trimming|trim|VBG|_ -LRB-|-lrb-|-LRB-|_ cut-off|cut-off|JJ|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ adapter|adapter|NN|_ removal|removal|NN|_ using|use|VBG|_ cutadapt|cutadapt|JJ|_ 1.15|1.15|CD|_
generattion|generattion|NN|_ of|of|IN|_ reverse|reverse|JJ|_ complement|complement|NN|_ reads|read|VBZ|_ using|use|VBG|_ FASTX|FASTX|NNP|_ 0.0.14|0.0.14|CD|_
poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ φO104|φo104|NN|_ and|and|CC|_ φPA8|φpa8|NN|_ genomes|genome|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ -LRB-|-lrb-|-LRB-|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ with|with|IN|_ the|the|DT|_ locations|location|NNS|_ of|of|IN|_ the|the|DT|_ annotation|annotation|NN|_ entries|entry|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ qunatification|qunatification|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ annotation|annotation|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ DESeq2|deseq2|NN|_ 1.16.1|1.16.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ φPA8|φpa8|NN|_ -LRB-|-lrb-|-LRB-|_ KP682374|kp682374|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ φO104|φo104|NN|_ -LRB-|-lrb-|-LRB-|_ 3256115|3256115|CD|_ to|to|TO|_ 3317011|3317011|CD|_ from|from|IN|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ of|of|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ data|datum|NNS|_ used|use|VBN|_ for|for|IN|_ DESeq2|deseq2|NN|_ analysis|analysis|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RiboLock|RiboLock|NNP|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ further|further|JJ|_ treated|treat|VBN|_ with|with|IN|_ RiboZero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ Qubit|qubit|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ :|:|:|_ :|:|:|_ φO104|φo104|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ phageO104|phageo104|NN|_ in|in|IN|_ the|the|DT|_ wrbA|wrba|NN|GEN gene|gene|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ :|:|:|_ :|:|:|_ φO104|φo104|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
Petya|petya|NN|_ ,|,|,|_ ,|,|,|_ Berger|Berger|NNP|_
quality|quality|NN|_ trimming|trim|VBG|_ -LRB-|-lrb-|-LRB-|_ cut-off|cut-off|JJ|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ adapter|adapter|NN|_ removal|removal|NN|_ using|use|VBG|_ cutadapt|cutadapt|JJ|_ 1.15|1.15|CD|_
generattion|generattion|NN|_ of|of|IN|_ reverse|reverse|JJ|_ complement|complement|NN|_ reads|read|VBZ|_ using|use|VBG|_ FASTX|FASTX|NNP|_ 0.0.14|0.0.14|CD|_
poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ φO104|φo104|NN|_ and|and|CC|_ φPA8|φpa8|NN|_ genomes|genome|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ -LRB-|-lrb-|-LRB-|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ with|with|IN|_ the|the|DT|_ locations|location|NNS|_ of|of|IN|_ the|the|DT|_ annotation|annotation|NN|_ entries|entry|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ qunatification|qunatification|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ annotation|annotation|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ DESeq2|deseq2|NN|_ 1.16.1|1.16.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ φPA8|φpa8|NN|_ -LRB-|-lrb-|-LRB-|_ KP682374|kp682374|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ φO104|φo104|NN|_ -LRB-|-lrb-|-LRB-|_ 3256115|3256115|CD|_ to|to|TO|_ 3317011|3317011|CD|_ from|from|IN|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ of|of|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ data|datum|NNS|_ used|use|VBN|_ for|for|IN|_ DESeq2|deseq2|NN|_ analysis|analysis|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RiboLock|RiboLock|NNP|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ further|further|JJ|_ treated|treat|VBN|_ with|with|IN|_ RiboZero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ Qubit|qubit|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ :|:|:|_ :|:|:|_ φO104|φo104|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ phageO104|phageo104|NN|_ in|in|IN|_ the|the|DT|_ wrbA|wrba|NN|GEN gene|gene|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ :|:|:|_ :|:|:|_ φO104|φo104|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
Petya|petya|NN|_ ,|,|,|_ ,|,|,|_ Berger|Berger|NNP|_
quality|quality|NN|_ trimming|trim|VBG|_ -LRB-|-lrb-|-LRB-|_ cut-off|cut-off|JJ|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ adapter|adapter|NN|_ removal|removal|NN|_ using|use|VBG|_ cutadapt|cutadapt|JJ|_ 1.15|1.15|CD|_
generattion|generattion|NN|_ of|of|IN|_ reverse|reverse|JJ|_ complement|complement|NN|_ reads|read|VBZ|_ using|use|VBG|_ FASTX|FASTX|NNP|_ 0.0.14|0.0.14|CD|_
poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ φO104|φo104|NN|_ and|and|CC|_ φPA8|φpa8|NN|_ genomes|genome|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ -LRB-|-lrb-|-LRB-|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ with|with|IN|_ the|the|DT|_ locations|location|NNS|_ of|of|IN|_ the|the|DT|_ annotation|annotation|NN|_ entries|entry|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ qunatification|qunatification|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ annotation|annotation|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ DESeq2|deseq2|NN|_ 1.16.1|1.16.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ φPA8|φpa8|NN|_ -LRB-|-lrb-|-LRB-|_ KP682374|kp682374|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ φO104|φo104|NN|_ -LRB-|-lrb-|-LRB-|_ 3256115|3256115|CD|_ to|to|TO|_ 3317011|3317011|CD|_ from|from|IN|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ of|of|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ data|datum|NNS|_ used|use|VBN|_ for|for|IN|_ DESeq2|deseq2|NN|_ analysis|analysis|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RiboLock|RiboLock|NNP|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ further|further|JJ|_ treated|treat|VBN|_ with|with|IN|_ RiboZero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ Qubit|qubit|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ φPA8|φpa8|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ phagePA8|phagepa8|NN|_ in|in|IN|_ the|the|DT|_ argW|argw|NN|GEN gene|gene|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ φPA8|φpa8|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
Petya|petya|NN|_ ,|,|,|_ ,|,|,|_ Berger|Berger|NNP|_
quality|quality|NN|_ trimming|trim|VBG|_ -LRB-|-lrb-|-LRB-|_ cut-off|cut-off|JJ|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ adapter|adapter|NN|_ removal|removal|NN|_ using|use|VBG|_ cutadapt|cutadapt|JJ|_ 1.15|1.15|CD|_
generattion|generattion|NN|_ of|of|IN|_ reverse|reverse|JJ|_ complement|complement|NN|_ reads|read|VBZ|_ using|use|VBG|_ FASTX|FASTX|NNP|_ 0.0.14|0.0.14|CD|_
poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ φO104|φo104|NN|_ and|and|CC|_ φPA8|φpa8|NN|_ genomes|genome|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ -LRB-|-lrb-|-LRB-|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ with|with|IN|_ the|the|DT|_ locations|location|NNS|_ of|of|IN|_ the|the|DT|_ annotation|annotation|NN|_ entries|entry|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ qunatification|qunatification|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ annotation|annotation|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ DESeq2|deseq2|NN|_ 1.16.1|1.16.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ φPA8|φpa8|NN|_ -LRB-|-lrb-|-LRB-|_ KP682374|kp682374|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ φO104|φo104|NN|_ -LRB-|-lrb-|-LRB-|_ 3256115|3256115|CD|_ to|to|TO|_ 3317011|3317011|CD|_ from|from|IN|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ of|of|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ data|datum|NNS|_ used|use|VBN|_ for|for|IN|_ DESeq2|deseq2|NN|_ analysis|analysis|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RiboLock|RiboLock|NNP|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ further|further|JJ|_ treated|treat|VBN|_ with|with|IN|_ RiboZero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ Qubit|qubit|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ φPA8|φpa8|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ phagePA8|phagepa8|NN|_ in|in|IN|_ the|the|DT|_ argW|argw|NN|GEN gene|gene|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ φPA8|φpa8|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
Petya|petya|NN|_ ,|,|,|_ ,|,|,|_ Berger|Berger|NNP|_
quality|quality|NN|_ trimming|trim|VBG|_ -LRB-|-lrb-|-LRB-|_ cut-off|cut-off|JJ|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ adapter|adapter|NN|_ removal|removal|NN|_ using|use|VBG|_ cutadapt|cutadapt|JJ|_ 1.15|1.15|CD|_
generattion|generattion|NN|_ of|of|IN|_ reverse|reverse|JJ|_ complement|complement|NN|_ reads|read|VBZ|_ using|use|VBG|_ FASTX|FASTX|NNP|_ 0.0.14|0.0.14|CD|_
poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ φO104|φo104|NN|_ and|and|CC|_ φPA8|φpa8|NN|_ genomes|genome|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ -LRB-|-lrb-|-LRB-|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ with|with|IN|_ the|the|DT|_ locations|location|NNS|_ of|of|IN|_ the|the|DT|_ annotation|annotation|NN|_ entries|entry|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_
differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ qunatification|qunatification|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ annotation|annotation|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.4.3|0.4.3|CD|_ and|and|CC|_ DESeq2|deseq2|NN|_ 1.16.1|1.16.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ φPA8|φpa8|NN|_ -LRB-|-lrb-|-LRB-|_ KP682374|kp682374|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ φO104|φo104|NN|_ -LRB-|-lrb-|-LRB-|_ 3256115|3256115|CD|_ to|to|TO|_ 3317011|3317011|CD|_ from|from|IN|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ of|of|IN|_ the|the|DT|_ gene|gene|NN|_ wise|wise|JJ|_ quantification|quantification|NN|_ data|datum|NNS|_ used|use|VBN|_ for|for|IN|_ DESeq2|deseq2|NN|_ analysis|analysis|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RiboLock|RiboLock|NNP|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ further|further|JJ|_ treated|treat|VBN|_ with|with|IN|_ RiboZero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ Qubit|qubit|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ φPA8|φpa8|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ phagePA8|phagepa8|NN|_ in|in|IN|_ the|the|DT|_ argW|argw|NN|GEN gene|gene|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ till|till|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ φPA8|φpa8|NN|_
After|after|IN|_ the|the|DT|_ treatment|treatment|NN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ lysed|lyse|VBN|_ with|with|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ ml|ml|NN|_ of|of|IN|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ C|c|NN|_ till|till|IN|_ the|the|DT|_ RNA|rna|NN|_ isolation|isolation|NN|_ protocol|protocol|NN|_ was|be|VBD|_ resumed|resume|VBN|_ .|.|.|_
Petya|petya|NN|_ ,|,|,|_ ,|,|,|_ Berger|Berger|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|VBD|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|VBD|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|VBD|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|VBD|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|JJ|_ _|_|NN|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|JJ|_ _|_|NN|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|JJ|_ _|_|NN|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|JJ|_ _|_|NN|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
GMOS|gmo|NNS|_ _|_|VBP|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
GMOS|gmo|NNS|_ _|_|VBP|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
GMOS|gmo|NNS|_ _|_|VBP|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
GMOS|gmo|NNS|_ _|_|VBP|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
GMOS|gmo|NNS|_ _|_|VBP|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
GMOS|gmo|NNS|_ _|_|VBP|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|EC|NNP|_ ALE-1|ALE-1|NNP|_ _|_|SYM|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|EC|NNP|_ ALE-1|ALE-1|NNP|_ _|_|SYM|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|EC|NNP|_ ALE-1|ALE-1|NNP|_ _|_|SYM|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|EC|NNP|_ ALE-1|ALE-1|NNP|_ _|_|SYM|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-1|ale-1|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-1|ale-1|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-1|ale-1|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-1|ale-1|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-2|ale-2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-2|ale-2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-2|ale-2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-2|ale-2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-2|ale-2|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-2|ale-2|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-2|ale-2|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-2|ale-2|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|EC|NNP|_ ALE-3|ALE-3|NNP|_ _|_|SYM|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|EC|NNP|_ ALE-3|ALE-3|NNP|_ _|_|SYM|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|EC|NNP|_ ALE-3|ALE-3|NNP|_ _|_|SYM|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|EC|NNP|_ ALE-3|ALE-3|NNP|_ _|_|SYM|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-3|ale-3|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-3|ale-3|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-3|ale-3|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-3|ale-3|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-4|ale-4|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-4|ale-4|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-4|ale-4|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-4|ale-4|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-4|ale-4|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-4|ale-4|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
The|The|NNP|_ base|base|NN|_ calling|call|VBG|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ v2|v2|NN|_ .7.7|.7.7|CD|_ ;|;|:|_ data|datum|NNS|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ fastq|fastq|NN|_ and|and|CC|_ demultiplexed|demultiplex|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ bcl2fastq2|bcl2fastq2|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v2|v2|NN|_ .20|.20|CD|_ ;|;|:|_
Sequence|sequence|NN|_ reads|read|VBZ|_ generated|generate|VBN|_ from|from|IN|_ RNA-Seq|rna-seq|NN|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ with|with|IN|_ default|default|NN|_ options|option|NNS|_ to|to|TO|_ generate|generate|VB|_ SAM|sam|NN|_ output|output|NN|_ files|file|NNS|_
Transcript|Transcript|NNP|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|GenomicAlignments|NNP|_ package|package|NN|_ with|with|IN|_ strand|strand|NN|_ inversion|inversion|NN|_ for|for|IN|_ the|the|DT|_ dUTP|dutp|NN|_ protocol|protocol|NN|_ and|and|CC|_ strict|strict|JJ|_ intersection|intersection|NN|_ mode|mode|NN|_
Estimated|estimate|VBN|_ the|the|DT|_ dispersion|dispersion|NN|_ of|of|IN|_ each|each|DT|_ gene|gene|NN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
Transcript|transcript|NN|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ DESeq2|deseq2|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
KAPA|KAPA|NNP|_ Stranded|Stranded|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-4|ale-4|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED w|w|NN|_ /|/|:|_ 4g/L|4g/l|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 100X|100x|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ agitation|agitation|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ the|the|DT|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ fresh|fresh|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ agitation|agitation|NN|_ to|to|TO|_ the|the|DT|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
EC|ec|NN|_ ALE-4|ale-4|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|CD|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ bacteria|bacterium|NNS|_ culture|culture|NN|_
Amitesh|amitesh|NN|_ ,|,|,|_ ,|,|,|_ Anand|Anand|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED +|+|CC|_ 5|5|CD|_ %|%|NN|_ ethanol|ethanol|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ baeR|baer|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ baeR|baer|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED +|+|CC|_ 5|5|CD|_ %|%|NN|_ ethanol|ethanol|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ baeR|baer|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ cpxR|cpxr|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ cpxR|cpxr|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ TMA|tma|NN|_ +|+|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ kdpE|kdpe|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ TMA|tma|NN|_ +|+|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ kdpE|kdpe|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ TMA|tma|NN|_ +|+|CC|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ kdpE|kdpe|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ TMA|tma|NN|_ +|+|CC|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ kdpE|kdpe|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ TMA|tma|NN|_ +|+|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ TMA|tma|NN|_ +|+|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ TMA|tma|NN|_ +|+|CC|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ TMA|tma|NN|_ +|+|CC|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ phoB|phob|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ phoB|phob|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ phoB|phob|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ phoB|phob|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ zraR|zrar|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED +|+|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ zraR|zrar|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED +|+|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ zraR|zrar|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED +|+|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
RNA-seq|rna-seq|NN|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.1.2|1.1.2|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ ``|``|``|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ −|−|CD|_ 3|3|CD|_ 3|3|CD|_ ''|''|''|_ .|.|.|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ summarizeOverlaps|summarizeoverlap|NNS|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ GenomicAlignments|genomicalignment|NNS|_ package|package|NN|_ ,|,|,|_ using|use|VBG|_ options|option|NNS|_ ``|``|``|_ mode|mode|NN|_ =|=|JJ|_ ``|``|``|_ IntersectionStrict|IntersectionStrict|NNP|_ ''|''|''|_ ,|,|,|_ singleEnd|singleend|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ ignore.strand|ignore.strand|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ preprocess.reads|preprocess.reads|NNS|_ =|=|JJ|_ invertStrand|invertstrand|NN|_ ''|''|''|_
Transcripts|transcript|NNS|_ per|per|IN|_ Million|Million|NNP|_ -LRB-|-lrb-|-LRB-|_ TPM|TPM|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ 's|'s|POS|_ fpkm|fpkm|NN|_ function|function|NN|_ ,|,|,|_ then|then|RB|_ normalizing|normalize|VBG|_ for|for|IN|_ library|library|NN|_ size|size|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NNS|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ Transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ 3|3|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 6|6|CD|_ mL|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ Quick|Quick|NNP|_ RNA|rna|NN|_ fungal/bacterial|fungal/bacterial|NN|_ microprep|microprep|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instructions|instruction|NNS|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ preparations|preparation|NNS|_ using|use|VBG|_ RNase|rnase|NN|_ H.|H.|NNP|_ First|First|NNP|_ ,|,|,|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ secondary|secondary|JJ|_ structures|structure|NNS|_ in|in|IN|_ the|the|DT|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ 32-mer|32-mer|JJ|_ DNA|dna|NN|_ oligonucleotide|oligonucleotide|NN|_ probes|probe|NNS|_ complementary|complementary|JJ|_ to|to|TO|_ 5S|5s|NN|_ ,|,|,|_ 16S|16s|NN|_ ,|,|,|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ subunits|subunit|NNS|_ and|and|CC|_ spaced|space|VBD|_ nine|nine|CD|_ bases|basis|NNS|_ apart|apart|RB|_ were|be|VBD|_ then|then|RB|_ annealed|anneal|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ followed|follow|VBN|_ by|by|IN|_ digestion|digestion|NN|_ with|with|IN|_ Hybridase|hybridase|NN|_ -LRB-|-lrb-|-LRB-|_ Lucigen|lucigen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ thermostable|thermostable|JJ|_ RNase|rnase|NN|_ H.|h.|NN|_ Hybridase|hybridase|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ the|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ at|at|IN|_ that|that|DT|_ temperature|temperature|NN|_ ,|,|,|_ then|then|RB|_ heated|heat|VBN|_ again|again|RB|_ to|to|TO|_ 90|90|CD|_ °C|°c|NN|_ for|for|IN|_ one|one|CD|_ second|second|JJ|_ to|to|TO|_ remove|remove|VB|_ remaining|remain|VBG|_ secondary|secondary|JJ|_ structures|structure|NNS|_ ,|,|,|_ and|and|CC|_ finally|finally|RB|_ returned|return|VBD|_ to|to|TO|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ quickly|quickly|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ guanidine|guanidine|NN|_ thiocyanate|thiocyanate|NN|_ while|while|IN|_ still|still|RB|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ before|before|IN|_ purifying|purify|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ with|with|IN|_ a|a|DT|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ kit|kit|NN|_ using|use|VBG|_ their|they|PRP$|_ 200|200|CD|_ nt|nt|NN|_ cutoff|cutoff|NN|_ protocol|protocol|NN|_ .|.|.|_ Carryover|carryover|NN|_ oligos|oligo|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ a|a|DT|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ which|which|WDT|_ was|be|VBD|_ started|start|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ gradually|gradually|RB|_ increased|increase|VBN|_ to|to|TO|_ 42|42|CD|_ °C|°c|NN|_ over|over|IN|_ a|a|DT|_ half|half|JJ|_ hour|hour|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ up|up|RP|_ with|with|IN|_ another|another|DT|_ column|column|NN|_ purification|purification|NN|_ as|as|IN|_ stated|state|VBN|_ above|above|IN|_ .|.|.|_
Paired-end|paired-end|NN|_ library|library|NN|_ preparation|preparation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ KAPA|kapa|NN|_ RNA|rna|NN|_ HyperPrep|hyperprep|NN|_ kit|kit|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED +|+|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
For|for|IN|_ ethanol|ethanol|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ BaeR|baer|NN|TF and|and|CC|_ CpxR|cpxr|NN|TF -RRB-|-rrb-|-RRB-|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ then|then|RB|_ ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ before|before|IN|_ being|be|VBG|_ collected|collect|VBN|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|RNA-seq|NNP|_ .|.|.|_ For|for|IN|_ KdpDE|kdpde|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ Tris|Tris|NNP|_ maleic|maleic|JJ|_ acid|acid|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ TMA|tma|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 115|115|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ TMA|tma|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ TMA|tma|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ Glucose|glucose|NN|_ and|and|CC|_ collected|collect|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ and|and|CC|_ RNA-seq|rna-seq|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ PhoRB|phorb|NN|_ :|:|:|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED without|without|IN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ M9-P|m9-p|NN|_ ;|;|:|_ without|without|IN|_ Na2HPO4|na2hpo4|NN|_ and|and|CC|_ KH2PO4|kh2po4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ in|in|IN|_ M9-P|m9-p|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ about|about|IN|_ the|the|DT|_ doubling|double|VBG|_ time|time|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ ZraSR|zrasr|NN|_ :|:|:|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ 1|1|CD|_ mM|mm|NN|KWSUPP ZnCl2|zncl2|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O.|O.|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ RTA|rta|NN|_ 1.18|1.18|CD|_ .|.|.|_
Adaptor|adaptor|NN|_ and|and|CC|_ barcode|barcode|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ cutadapt|cutadapt|JJ|_ 1.18|1.18|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ duplicates|duplicate|VBZ|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ bbmap|bbmap|NN|_ 38.22|38.22|CD|_ .|.|.|_
RNET-seq|rnet-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.2.2|1.2.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ q|q|SYM|_ -|-|:|_ p|p|NN|_ 10|10|CD|_ -|-|:|_ v|v|LS|_ 1|1|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ .|.|.|_ RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ by|by|IN|_ STAR|star|NN|_ 2.6.1|2.6.1|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ were|be|VBD|_ recorded|record|VBN|_ and|and|CC|_ counted|count|VBN|_ in|in|IN|_ each|each|DT|_ coordinate|coordinate|NN|_ by|by|IN|_ bedtools|bedtool|NNS|_ 2.27.1|2.27.1|CD|_ .|.|.|_ For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ aligned|align|VBN|_ reads|read|VBZ|_ in|in|IN|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ HTseq|htseq|NN|_ 0.11.2|0.11.2|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|MG1655|NNP|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ _|_|SYM|_ strand.wig|strand.wig|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ wig|wig|NN|_ files|file|NNS|_ ,|,|,|_ the|the|DT|_ scores|score|NNS|_ represent|represent|VBP|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ hRpoD|hrpod|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ hRpoDgreAB|hrpodgreab|NN|_ -|-|:|_ _|_|SYM|_ TPM.csv|TPM.csv|NNP|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ TMP|tmp|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 4|4|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ ºC|ºc|NN|_ to|to|TO|_ disrupt|disrupt|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ PCI|pci|NN|_ extraction|extraction|NN|_ and|and|CC|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ isopropanol|isopropanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ top|top|JJ|_ water|water|NN|_ phase|phase|NN|_ to|to|TO|_ precipitate|precipitate|VB|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ 50|50|CD|_ U|U|NNP|_ DNase|dnase|NN|_ I|i|CD|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ by|by|IN|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ Standard|Standard|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoD|hrpod|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ sigma70|sigma70|CD|_ WT|WT|NNP|_
genotype|genotype|NN|_ :|:|:|_ W3110|w3110|NN|_ 6xHis-rpoD|6xhis-rpod|JJ|_
growth|growth|NN|_ :|:|:|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ in|in|IN|_ LB|LB|NNP|_
The|The|NNP|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoD|hrpod|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
Zhe|Zhe|NNP|_ ,|,|,|_ ,|,|,|_ Sun|Sun|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ RTA|rta|NN|_ 1.18|1.18|CD|_ .|.|.|_
Adaptor|adaptor|NN|_ and|and|CC|_ barcode|barcode|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ cutadapt|cutadapt|JJ|_ 1.18|1.18|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ duplicates|duplicate|VBZ|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ bbmap|bbmap|NN|_ 38.22|38.22|CD|_ .|.|.|_
RNET-seq|rnet-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.2.2|1.2.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ q|q|SYM|_ -|-|:|_ p|p|NN|_ 10|10|CD|_ -|-|:|_ v|v|LS|_ 1|1|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ .|.|.|_ RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ by|by|IN|_ STAR|star|NN|_ 2.6.1|2.6.1|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ were|be|VBD|_ recorded|record|VBN|_ and|and|CC|_ counted|count|VBN|_ in|in|IN|_ each|each|DT|_ coordinate|coordinate|NN|_ by|by|IN|_ bedtools|bedtool|NNS|_ 2.27.1|2.27.1|CD|_ .|.|.|_ For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ aligned|align|VBN|_ reads|read|VBZ|_ in|in|IN|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ HTseq|htseq|NN|_ 0.11.2|0.11.2|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|MG1655|NNP|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ _|_|SYM|_ strand.wig|strand.wig|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ wig|wig|NN|_ files|file|NNS|_ ,|,|,|_ the|the|DT|_ scores|score|NNS|_ represent|represent|VBP|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ hRpoD|hrpod|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ hRpoDgreAB|hrpodgreab|NN|_ -|-|:|_ _|_|SYM|_ TPM.csv|TPM.csv|NNP|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ TMP|tmp|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 4|4|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ ºC|ºc|NN|_ to|to|TO|_ disrupt|disrupt|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ PCI|pci|NN|_ extraction|extraction|NN|_ and|and|CC|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ isopropanol|isopropanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ top|top|JJ|_ water|water|NN|_ phase|phase|NN|_ to|to|TO|_ precipitate|precipitate|VB|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ 50|50|CD|_ U|U|NNP|_ DNase|dnase|NN|_ I|i|CD|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ by|by|IN|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ Standard|Standard|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoD|hrpod|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ sigma70|sigma70|CD|_ WT|WT|NNP|_
genotype|genotype|NN|_ :|:|:|_ W3110|w3110|NN|_ 6xHis-rpoD|6xhis-rpod|JJ|_
growth|growth|NN|_ :|:|:|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ in|in|IN|_ LB|LB|NNP|_
The|The|NNP|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoD|hrpod|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
Zhe|Zhe|NNP|_ ,|,|,|_ ,|,|,|_ Sun|Sun|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ RTA|rta|NN|_ 1.18|1.18|CD|_ .|.|.|_
Adaptor|adaptor|NN|_ and|and|CC|_ barcode|barcode|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ cutadapt|cutadapt|JJ|_ 1.18|1.18|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ duplicates|duplicate|VBZ|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ bbmap|bbmap|NN|_ 38.22|38.22|CD|_ .|.|.|_
RNET-seq|rnet-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.2.2|1.2.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ q|q|SYM|_ -|-|:|_ p|p|NN|_ 10|10|CD|_ -|-|:|_ v|v|LS|_ 1|1|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ .|.|.|_ RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ by|by|IN|_ STAR|star|NN|_ 2.6.1|2.6.1|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ were|be|VBD|_ recorded|record|VBN|_ and|and|CC|_ counted|count|VBN|_ in|in|IN|_ each|each|DT|_ coordinate|coordinate|NN|_ by|by|IN|_ bedtools|bedtool|NNS|_ 2.27.1|2.27.1|CD|_ .|.|.|_ For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ aligned|align|VBN|_ reads|read|VBZ|_ in|in|IN|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ HTseq|htseq|NN|_ 0.11.2|0.11.2|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|MG1655|NNP|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ _|_|SYM|_ strand.wig|strand.wig|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ wig|wig|NN|_ files|file|NNS|_ ,|,|,|_ the|the|DT|_ scores|score|NNS|_ represent|represent|VBP|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ hRpoD|hrpod|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ hRpoDgreAB|hrpodgreab|NN|_ -|-|:|_ _|_|SYM|_ TPM.csv|TPM.csv|NNP|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ TMP|tmp|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 4|4|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ ºC|ºc|NN|_ to|to|TO|_ disrupt|disrupt|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ PCI|pci|NN|_ extraction|extraction|NN|_ and|and|CC|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ isopropanol|isopropanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ top|top|JJ|_ water|water|NN|_ phase|phase|NN|_ to|to|TO|_ precipitate|precipitate|VB|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ 50|50|CD|_ U|U|NNP|_ DNase|dnase|NN|_ I|i|CD|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ by|by|IN|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ Standard|Standard|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoD|hrpod|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ sigma70|sigma70|CD|_ WT|WT|NNP|_
genotype|genotype|NN|_ :|:|:|_ W3110|w3110|NN|_ 6xHis-rpoD|6xhis-rpod|JJ|_
growth|growth|NN|_ :|:|:|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ in|in|IN|_ LB|LB|NNP|_
The|The|NNP|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoD|hrpod|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
Zhe|Zhe|NNP|_ ,|,|,|_ ,|,|,|_ Sun|Sun|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ RTA|rta|NN|_ 1.18|1.18|CD|_ .|.|.|_
Adaptor|adaptor|NN|_ and|and|CC|_ barcode|barcode|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ cutadapt|cutadapt|JJ|_ 1.18|1.18|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ duplicates|duplicate|VBZ|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ bbmap|bbmap|NN|_ 38.22|38.22|CD|_ .|.|.|_
RNET-seq|rnet-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.2.2|1.2.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ q|q|SYM|_ -|-|:|_ p|p|NN|_ 10|10|CD|_ -|-|:|_ v|v|LS|_ 1|1|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ .|.|.|_ RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ by|by|IN|_ STAR|star|NN|_ 2.6.1|2.6.1|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ were|be|VBD|_ recorded|record|VBN|_ and|and|CC|_ counted|count|VBN|_ in|in|IN|_ each|each|DT|_ coordinate|coordinate|NN|_ by|by|IN|_ bedtools|bedtool|NNS|_ 2.27.1|2.27.1|CD|_ .|.|.|_ For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ aligned|align|VBN|_ reads|read|VBZ|_ in|in|IN|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ HTseq|htseq|NN|_ 0.11.2|0.11.2|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|MG1655|NNP|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ _|_|SYM|_ strand.wig|strand.wig|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ wig|wig|NN|_ files|file|NNS|_ ,|,|,|_ the|the|DT|_ scores|score|NNS|_ represent|represent|VBP|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ hRpoD|hrpod|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ hRpoDgreAB|hrpodgreab|NN|_ -|-|:|_ _|_|SYM|_ TPM.csv|TPM.csv|NNP|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ TMP|tmp|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 4|4|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ ºC|ºc|NN|_ to|to|TO|_ disrupt|disrupt|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ PCI|pci|NN|_ extraction|extraction|NN|_ and|and|CC|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ isopropanol|isopropanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ top|top|JJ|_ water|water|NN|_ phase|phase|NN|_ to|to|TO|_ precipitate|precipitate|VB|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ 50|50|CD|_ U|U|NNP|_ DNase|dnase|NN|_ I|i|CD|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ by|by|IN|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ Standard|Standard|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoDΔgreAB|hrpodδgreab|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ sigma70|sigma70|NN|_ greAB|greab|NN|_ -|-|:|_
genotype|genotype|NN|_ :|:|:|_ W3110|w3110|NN|_ 6xHis-rpoD|6xhis-rpod|NN|_ greA|grea|NN|GEN :|:|:|_ :|:|:|_ tet|tet|NN|_ greB|greb|NN|GEN :|:|:|_ :|:|:|_ amp|amp|NN|_
growth|growth|NN|_ :|:|:|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ in|in|IN|_ LB|LB|NNP|_
The|The|NNP|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoDΔgreAB|hrpodδgreab|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
Zhe|Zhe|NNP|_ ,|,|,|_ ,|,|,|_ Sun|Sun|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ RTA|rta|NN|_ 1.18|1.18|CD|_ .|.|.|_
Adaptor|adaptor|NN|_ and|and|CC|_ barcode|barcode|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ cutadapt|cutadapt|JJ|_ 1.18|1.18|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ duplicates|duplicate|VBZ|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ bbmap|bbmap|NN|_ 38.22|38.22|CD|_ .|.|.|_
RNET-seq|rnet-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.2.2|1.2.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ q|q|SYM|_ -|-|:|_ p|p|NN|_ 10|10|CD|_ -|-|:|_ v|v|LS|_ 1|1|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ .|.|.|_ RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ by|by|IN|_ STAR|star|NN|_ 2.6.1|2.6.1|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ were|be|VBD|_ recorded|record|VBN|_ and|and|CC|_ counted|count|VBN|_ in|in|IN|_ each|each|DT|_ coordinate|coordinate|NN|_ by|by|IN|_ bedtools|bedtool|NNS|_ 2.27.1|2.27.1|CD|_ .|.|.|_ For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ aligned|align|VBN|_ reads|read|VBZ|_ in|in|IN|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ HTseq|htseq|NN|_ 0.11.2|0.11.2|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|MG1655|NNP|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ _|_|SYM|_ strand.wig|strand.wig|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ wig|wig|NN|_ files|file|NNS|_ ,|,|,|_ the|the|DT|_ scores|score|NNS|_ represent|represent|VBP|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ hRpoD|hrpod|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ hRpoDgreAB|hrpodgreab|NN|_ -|-|:|_ _|_|SYM|_ TPM.csv|TPM.csv|NNP|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ TMP|tmp|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 4|4|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ ºC|ºc|NN|_ to|to|TO|_ disrupt|disrupt|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ PCI|pci|NN|_ extraction|extraction|NN|_ and|and|CC|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ isopropanol|isopropanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ top|top|JJ|_ water|water|NN|_ phase|phase|NN|_ to|to|TO|_ precipitate|precipitate|VB|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ 50|50|CD|_ U|U|NNP|_ DNase|dnase|NN|_ I|i|CD|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ by|by|IN|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ Standard|Standard|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoDΔgreAB|hrpodδgreab|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ sigma70|sigma70|NN|_ greAB|greab|NN|_ -|-|:|_
genotype|genotype|NN|_ :|:|:|_ W3110|w3110|NN|_ 6xHis-rpoD|6xhis-rpod|NN|_ greA|grea|NN|GEN :|:|:|_ :|:|:|_ tet|tet|NN|_ greB|greb|NN|GEN :|:|:|_ :|:|:|_ amp|amp|NN|_
growth|growth|NN|_ :|:|:|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ in|in|IN|_ LB|LB|NNP|_
The|The|NNP|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoDΔgreAB|hrpodδgreab|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
Zhe|Zhe|NNP|_ ,|,|,|_ ,|,|,|_ Sun|Sun|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ RTA|rta|NN|_ 1.18|1.18|CD|_ .|.|.|_
Adaptor|adaptor|NN|_ and|and|CC|_ barcode|barcode|NN|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ cutadapt|cutadapt|JJ|_ 1.18|1.18|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ duplicates|duplicate|VBZ|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ bbmap|bbmap|NN|_ 38.22|38.22|CD|_ .|.|.|_
RNET-seq|rnet-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ using|use|VBG|_ bowtie|bowtie|NN|_ 1.2.2|1.2.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ q|q|SYM|_ -|-|:|_ p|p|NN|_ 10|10|CD|_ -|-|:|_ v|v|LS|_ 1|1|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ .|.|.|_ RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ by|by|IN|_ STAR|star|NN|_ 2.6.1|2.6.1|CD|_ .|.|.|_
For|for|IN|_ RNET-seq|rnet-seq|NN|_ ,|,|,|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ were|be|VBD|_ recorded|record|VBN|_ and|and|CC|_ counted|count|VBN|_ in|in|IN|_ each|each|DT|_ coordinate|coordinate|NN|_ by|by|IN|_ bedtools|bedtool|NNS|_ 2.27.1|2.27.1|CD|_ .|.|.|_ For|for|IN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ aligned|align|VBN|_ reads|read|VBZ|_ in|in|IN|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ HTseq|htseq|NN|_ 0.11.2|0.11.2|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|MG1655|NNP|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ _|_|SYM|_ strand.wig|strand.wig|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ wig|wig|NN|_ files|file|NNS|_ ,|,|,|_ the|the|DT|_ scores|score|NNS|_ represent|represent|VBP|_ the|the|DT|_ counts|count|NNS|_ of|of|IN|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ whose|whose|WP$|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ mapped|map|VBN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ hRpoD|hrpod|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ hRpoDgreAB|hrpodgreab|NN|_ -|-|:|_ _|_|SYM|_ TPM.csv|TPM.csv|NNP|_ :|:|:|_ Comma-separated|comma-separated|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ TMP|tmp|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 4|4|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ ºC|ºc|NN|_ to|to|TO|_ disrupt|disrupt|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ PCI|pci|NN|_ extraction|extraction|NN|_ and|and|CC|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ isopropanol|isopropanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ top|top|JJ|_ water|water|NN|_ phase|phase|NN|_ to|to|TO|_ precipitate|precipitate|VB|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ 50|50|CD|_ U|U|NNP|_ DNase|dnase|NN|_ I|i|CD|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ by|by|IN|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ Standard|Standard|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoDΔgreAB|hrpodδgreab|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ sigma70|sigma70|NN|_ greAB|greab|NN|_ -|-|:|_
genotype|genotype|NN|_ :|:|:|_ W3110|w3110|NN|_ 6xHis-rpoD|6xhis-rpod|NN|_ greA|grea|NN|GEN :|:|:|_ :|:|:|_ tet|tet|NN|_ greB|greb|NN|GEN :|:|:|_ :|:|:|_ amp|amp|NN|_
growth|growth|NN|_ :|:|:|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ in|in|IN|_ LB|LB|NNP|_
The|The|NNP|_ overnight|overnight|JJ|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ºC|ºc|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
hRpoDΔgreAB|hrpodδgreab|NN|_ _|_|CD|_ RNA-seq|rna-seq|NN|_
Zhe|Zhe|NNP|_ ,|,|,|_ ,|,|,|_ Sun|Sun|NNP|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ obtained|obtain|VBN|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ Pipeline|Pipeline|NNP|_ .|.|.|_ All|all|DT|_ reads|read|VBZ|_ mapping|mapping|NN|_ with|with|IN|_ two|two|CD|_ or|or|CC|_ fewer|fewer|JJR|_ mismatches|mismatch|NNS|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Repeated|repeated|JJ|_ sequences|sequence|NNS|_ were|be|VBD|_ ignored|ignore|VBN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ counts|count|NNS|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ ssrA|ssra|NN|GEN RNA|rna|NN|_ and|and|CC|_ then|then|RB|_ converted|convert|VBD|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_ A|a|DT|_ value|value|NN|_ of|of|IN|_ 1|1|CD|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ every|every|DT|_ count|count|NN|_ before|before|IN|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ conversion|conversion|NN|_ to|to|TO|_ avoid|avoid|VB|_ an|a|DT|_ undefined|undefined|JJ|_ logarithm|logarithm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ The|the|DT|_ lifetime|lifetime|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ the|the|DT|_ inverse|inverse|NN|_ of|of|IN|_ the|the|DT|_ slope|slope|NN|_ of|of|IN|_ a|a|DT|_ linear|linear|JJ|_ fit|fit|NN|_ to|to|TO|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_
The|the|DT|_ measured|measure|VBN|_ lifetime|lifetime|NN|_ of|of|IN|_ mRNA|mrna|NN|_ is|be|VBZ|_ available|available|JJ|_ as|as|IN|_ a|a|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ real_rna_life.txt|real_rna_life.txt|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ the|the|DT|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ lysates|lysate|NNS|_ by|by|IN|_ phenol/chloroform|phenol/chloroform|NN|_ method|method|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ MICROBExpress|microbexpress|NN|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ except|except|IN|_ RNA|rna|NN|_ was|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ A|a|DT|_ second|second|JJ|_ rRNA|rrna|NN|_ removal|removal|NN|_ step|step|NN|_ was|be|VBD|_ performed|perform|VBN|_ following|follow|VBG|_ the|the|DT|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Affymetrix|Affymetrix|NNP|_ Expression|expression|NN|_ Handbook|handbook|NN|_ ,|,|,|_ substituting|substitute|VBG|_ enzymes|enzyme|NNS|_ MMLV|mmlv|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNase|rnase|NN|_ H|h|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ DnaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Amplification|amplification|NN|_ grade|grade|NN|_ ,|,|,|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ Fragmentation|fragmentation|NN|_ Reagent|reagent|NN|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ collected|collect|VBN|_ by|by|IN|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ RNA|rna|NN|_ seq|seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ according|accord|VBG|_ to|to|TO|_ Illumna|Illumna|NNP|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ using|use|VBG|_ NEB|neb|NN|_ enzymes|enzyme|NNS|_ and|and|CC|_ barcoded|barcoded|JJ|_ adapters|adapter|NNS|_ -LRB-|-lrb-|-LRB-|_ Integrated|Integrated|NNP|_ DNA|DNA|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ with|with|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ GA|GA|NNP|_ II|II|NNP|_ machine|machine|NN|_ -LRB-|-lrb-|-LRB-|_ Center|center|NN|_ for|for|IN|_ Systems|Systems|NNP|_ Biology|Biology|NNP|_ ,|,|,|_ Harvard|Harvard|NNP|_ University|University|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.coli|e.coli|NNS|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug/ml|500ug/ml|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DY330|dy330|NN|_ -LRB-|-lrb-|-LRB-|_ W3110|w3110|NN|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP time|time|NN|_ point|point|NN|_ 0|0|CD|_
E.coli|e.coli|NN|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug/ml|500ug/ml|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_
Huiyi|Huiyi|NNP|_ ,|,|,|_ ,|,|,|_ Chen|Chen|NNP|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ obtained|obtain|VBN|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ Pipeline|Pipeline|NNP|_ .|.|.|_ All|all|DT|_ reads|read|VBZ|_ mapping|mapping|NN|_ with|with|IN|_ two|two|CD|_ or|or|CC|_ fewer|fewer|JJR|_ mismatches|mismatch|NNS|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Repeated|repeated|JJ|_ sequences|sequence|NNS|_ were|be|VBD|_ ignored|ignore|VBN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ counts|count|NNS|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ ssrA|ssra|NN|GEN RNA|rna|NN|_ and|and|CC|_ then|then|RB|_ converted|convert|VBD|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_ A|a|DT|_ value|value|NN|_ of|of|IN|_ 1|1|CD|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ every|every|DT|_ count|count|NN|_ before|before|IN|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ conversion|conversion|NN|_ to|to|TO|_ avoid|avoid|VB|_ an|a|DT|_ undefined|undefined|JJ|_ logarithm|logarithm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ The|the|DT|_ lifetime|lifetime|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ the|the|DT|_ inverse|inverse|NN|_ of|of|IN|_ the|the|DT|_ slope|slope|NN|_ of|of|IN|_ a|a|DT|_ linear|linear|JJ|_ fit|fit|NN|_ to|to|TO|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_
The|the|DT|_ measured|measure|VBN|_ lifetime|lifetime|NN|_ of|of|IN|_ mRNA|mrna|NN|_ is|be|VBZ|_ available|available|JJ|_ as|as|IN|_ a|a|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ real_rna_life.txt|real_rna_life.txt|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ the|the|DT|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ lysates|lysate|NNS|_ by|by|IN|_ phenol/chloroform|phenol/chloroform|NN|_ method|method|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ MICROBExpress|microbexpress|NN|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ except|except|IN|_ RNA|rna|NN|_ was|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ A|a|DT|_ second|second|JJ|_ rRNA|rrna|NN|_ removal|removal|NN|_ step|step|NN|_ was|be|VBD|_ performed|perform|VBN|_ following|follow|VBG|_ the|the|DT|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Affymetrix|Affymetrix|NNP|_ Expression|expression|NN|_ Handbook|handbook|NN|_ ,|,|,|_ substituting|substitute|VBG|_ enzymes|enzyme|NNS|_ MMLV|mmlv|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNase|rnase|NN|_ H|h|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ DnaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Amplification|amplification|NN|_ grade|grade|NN|_ ,|,|,|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ Fragmentation|fragmentation|NN|_ Reagent|reagent|NN|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ collected|collect|VBN|_ by|by|IN|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ RNA|rna|NN|_ seq|seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ according|accord|VBG|_ to|to|TO|_ Illumna|Illumna|NNP|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ using|use|VBG|_ NEB|neb|NN|_ enzymes|enzyme|NNS|_ and|and|CC|_ barcoded|barcoded|JJ|_ adapters|adapter|NNS|_ -LRB-|-lrb-|-LRB-|_ Integrated|Integrated|NNP|_ DNA|DNA|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ with|with|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ GA|GA|NNP|_ II|II|NNP|_ machine|machine|NN|_ -LRB-|-lrb-|-LRB-|_ Center|center|NN|_ for|for|IN|_ Systems|Systems|NNP|_ Biology|Biology|NNP|_ ,|,|,|_ Harvard|Harvard|NNP|_ University|University|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.coli|e.coli|NNS|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug/ml|500ug/ml|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DY330|dy330|NN|_ -LRB-|-lrb-|-LRB-|_ W3110|w3110|NN|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP time|time|NN|_ point|point|NN|_ 2|2|CD|_
E.coli|e.coli|NN|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug/ml|500ug/ml|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_
Huiyi|Huiyi|NNP|_ ,|,|,|_ ,|,|,|_ Chen|Chen|NNP|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ obtained|obtain|VBN|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ Pipeline|Pipeline|NNP|_ .|.|.|_ All|all|DT|_ reads|read|VBZ|_ mapping|mapping|NN|_ with|with|IN|_ two|two|CD|_ or|or|CC|_ fewer|fewer|JJR|_ mismatches|mismatch|NNS|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Repeated|repeated|JJ|_ sequences|sequence|NNS|_ were|be|VBD|_ ignored|ignore|VBN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ counts|count|NNS|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ ssrA|ssra|NN|GEN RNA|rna|NN|_ and|and|CC|_ then|then|RB|_ converted|convert|VBD|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_ A|a|DT|_ value|value|NN|_ of|of|IN|_ 1|1|CD|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ every|every|DT|_ count|count|NN|_ before|before|IN|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ conversion|conversion|NN|_ to|to|TO|_ avoid|avoid|VB|_ an|a|DT|_ undefined|undefined|JJ|_ logarithm|logarithm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ The|the|DT|_ lifetime|lifetime|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ the|the|DT|_ inverse|inverse|NN|_ of|of|IN|_ the|the|DT|_ slope|slope|NN|_ of|of|IN|_ a|a|DT|_ linear|linear|JJ|_ fit|fit|NN|_ to|to|TO|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_
The|the|DT|_ measured|measure|VBN|_ lifetime|lifetime|NN|_ of|of|IN|_ mRNA|mrna|NN|_ is|be|VBZ|_ available|available|JJ|_ as|as|IN|_ a|a|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ real_rna_life.txt|real_rna_life.txt|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ the|the|DT|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ lysates|lysate|NNS|_ by|by|IN|_ phenol/chloroform|phenol/chloroform|NN|_ method|method|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ MICROBExpress|microbexpress|NN|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ except|except|IN|_ RNA|rna|NN|_ was|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ A|a|DT|_ second|second|JJ|_ rRNA|rrna|NN|_ removal|removal|NN|_ step|step|NN|_ was|be|VBD|_ performed|perform|VBN|_ following|follow|VBG|_ the|the|DT|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Affymetrix|Affymetrix|NNP|_ Expression|expression|NN|_ Handbook|handbook|NN|_ ,|,|,|_ substituting|substitute|VBG|_ enzymes|enzyme|NNS|_ MMLV|mmlv|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNase|rnase|NN|_ H|h|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ DnaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Amplification|amplification|NN|_ grade|grade|NN|_ ,|,|,|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ Fragmentation|fragmentation|NN|_ Reagent|reagent|NN|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ collected|collect|VBN|_ by|by|IN|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ RNA|rna|NN|_ seq|seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ according|accord|VBG|_ to|to|TO|_ Illumna|Illumna|NNP|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ using|use|VBG|_ NEB|neb|NN|_ enzymes|enzyme|NNS|_ and|and|CC|_ barcoded|barcoded|JJ|_ adapters|adapter|NNS|_ -LRB-|-lrb-|-LRB-|_ Integrated|Integrated|NNP|_ DNA|DNA|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ with|with|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ GA|GA|NNP|_ II|II|NNP|_ machine|machine|NN|_ -LRB-|-lrb-|-LRB-|_ Center|center|NN|_ for|for|IN|_ Systems|Systems|NNP|_ Biology|Biology|NNP|_ ,|,|,|_ Harvard|Harvard|NNP|_ University|University|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.coli|e.coli|NNS|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug/ml|500ug/ml|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DY330|dy330|NN|_ -LRB-|-lrb-|-LRB-|_ W3110|w3110|NN|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP time|time|NN|_ point|point|NN|_ 4|4|CD|_
E.coli|e.coli|NN|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug/ml|500ug/ml|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_
Huiyi|Huiyi|NNP|_ ,|,|,|_ ,|,|,|_ Chen|Chen|NNP|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ obtained|obtain|VBN|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ Pipeline|Pipeline|NNP|_ .|.|.|_ All|all|DT|_ reads|read|VBZ|_ mapping|mapping|NN|_ with|with|IN|_ two|two|CD|_ or|or|CC|_ fewer|fewer|JJR|_ mismatches|mismatch|NNS|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Repeated|repeated|JJ|_ sequences|sequence|NNS|_ were|be|VBD|_ ignored|ignore|VBN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ counts|count|NNS|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ ssrA|ssra|NN|GEN RNA|rna|NN|_ and|and|CC|_ then|then|RB|_ converted|convert|VBD|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_ A|a|DT|_ value|value|NN|_ of|of|IN|_ 1|1|CD|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ every|every|DT|_ count|count|NN|_ before|before|IN|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ conversion|conversion|NN|_ to|to|TO|_ avoid|avoid|VB|_ an|a|DT|_ undefined|undefined|JJ|_ logarithm|logarithm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ The|the|DT|_ lifetime|lifetime|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ the|the|DT|_ inverse|inverse|NN|_ of|of|IN|_ the|the|DT|_ slope|slope|NN|_ of|of|IN|_ a|a|DT|_ linear|linear|JJ|_ fit|fit|NN|_ to|to|TO|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_
The|the|DT|_ measured|measure|VBN|_ lifetime|lifetime|NN|_ of|of|IN|_ mRNA|mrna|NN|_ is|be|VBZ|_ available|available|JJ|_ as|as|IN|_ a|a|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ real_rna_life.txt|real_rna_life.txt|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ the|the|DT|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ lysates|lysate|NNS|_ by|by|IN|_ phenol/chloroform|phenol/chloroform|NN|_ method|method|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ MICROBExpress|microbexpress|NN|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ except|except|IN|_ RNA|rna|NN|_ was|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ A|a|DT|_ second|second|JJ|_ rRNA|rrna|NN|_ removal|removal|NN|_ step|step|NN|_ was|be|VBD|_ performed|perform|VBN|_ following|follow|VBG|_ the|the|DT|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Affymetrix|Affymetrix|NNP|_ Expression|expression|NN|_ Handbook|handbook|NN|_ ,|,|,|_ substituting|substitute|VBG|_ enzymes|enzyme|NNS|_ MMLV|mmlv|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNase|rnase|NN|_ H|h|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ DnaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Amplification|amplification|NN|_ grade|grade|NN|_ ,|,|,|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ Fragmentation|fragmentation|NN|_ Reagent|reagent|NN|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ collected|collect|VBN|_ by|by|IN|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ RNA|rna|NN|_ seq|seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ according|accord|VBG|_ to|to|TO|_ Illumna|Illumna|NNP|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ using|use|VBG|_ NEB|neb|NN|_ enzymes|enzyme|NNS|_ and|and|CC|_ barcoded|barcoded|JJ|_ adapters|adapter|NNS|_ -LRB-|-lrb-|-LRB-|_ Integrated|Integrated|NNP|_ DNA|DNA|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ with|with|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ GA|GA|NNP|_ II|II|NNP|_ machine|machine|NN|_ -LRB-|-lrb-|-LRB-|_ Center|center|NN|_ for|for|IN|_ Systems|Systems|NNP|_ Biology|Biology|NNP|_ ,|,|,|_ Harvard|Harvard|NNP|_ University|University|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.coli|e.coli|NNS|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug/ml|500ug/ml|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DY330|dy330|NN|_ -LRB-|-lrb-|-LRB-|_ W3110|w3110|NN|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP time|time|NN|_ point|point|NN|_ 6|6|CD|_
E.coli|e.coli|NN|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug/ml|500ug/ml|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_
Huiyi|Huiyi|NNP|_ ,|,|,|_ ,|,|,|_ Chen|Chen|NNP|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ obtained|obtain|VBN|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ Pipeline|Pipeline|NNP|_ .|.|.|_ All|all|DT|_ reads|read|VBZ|_ mapping|mapping|NN|_ with|with|IN|_ two|two|CD|_ or|or|CC|_ fewer|fewer|JJR|_ mismatches|mismatch|NNS|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Repeated|repeated|JJ|_ sequences|sequence|NNS|_ were|be|VBD|_ ignored|ignore|VBN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ counts|count|NNS|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ ssrA|ssra|NN|GEN RNA|rna|NN|_ and|and|CC|_ then|then|RB|_ converted|convert|VBD|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_ A|a|DT|_ value|value|NN|_ of|of|IN|_ 1|1|CD|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ every|every|DT|_ count|count|NN|_ before|before|IN|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ conversion|conversion|NN|_ to|to|TO|_ avoid|avoid|VB|_ an|a|DT|_ undefined|undefined|JJ|_ logarithm|logarithm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ The|the|DT|_ lifetime|lifetime|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ the|the|DT|_ inverse|inverse|NN|_ of|of|IN|_ the|the|DT|_ slope|slope|NN|_ of|of|IN|_ a|a|DT|_ linear|linear|JJ|_ fit|fit|NN|_ to|to|TO|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_
The|the|DT|_ measured|measure|VBN|_ lifetime|lifetime|NN|_ of|of|IN|_ mRNA|mrna|NN|_ is|be|VBZ|_ available|available|JJ|_ as|as|IN|_ a|a|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ real_rna_life.txt|real_rna_life.txt|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ the|the|DT|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ lysates|lysate|NNS|_ by|by|IN|_ phenol/chloroform|phenol/chloroform|NN|_ method|method|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ MICROBExpress|microbexpress|NN|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ except|except|IN|_ RNA|rna|NN|_ was|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ A|a|DT|_ second|second|JJ|_ rRNA|rrna|NN|_ removal|removal|NN|_ step|step|NN|_ was|be|VBD|_ performed|perform|VBN|_ following|follow|VBG|_ the|the|DT|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Affymetrix|Affymetrix|NNP|_ Expression|expression|NN|_ Handbook|handbook|NN|_ ,|,|,|_ substituting|substitute|VBG|_ enzymes|enzyme|NNS|_ MMLV|mmlv|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNase|rnase|NN|_ H|h|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ DnaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Amplification|amplification|NN|_ grade|grade|NN|_ ,|,|,|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ Fragmentation|fragmentation|NN|_ Reagent|reagent|NN|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ collected|collect|VBN|_ by|by|IN|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ RNA|rna|NN|_ seq|seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ according|accord|VBG|_ to|to|TO|_ Illumna|Illumna|NNP|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ using|use|VBG|_ NEB|neb|NN|_ enzymes|enzyme|NNS|_ and|and|CC|_ barcoded|barcoded|JJ|_ adapters|adapter|NNS|_ -LRB-|-lrb-|-LRB-|_ Integrated|Integrated|NNP|_ DNA|DNA|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ with|with|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ GA|GA|NNP|_ II|II|NNP|_ machine|machine|NN|_ -LRB-|-lrb-|-LRB-|_ Center|center|NN|_ for|for|IN|_ Systems|Systems|NNP|_ Biology|Biology|NNP|_ ,|,|,|_ Harvard|Harvard|NNP|_ University|University|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.coli|e.coli|NNS|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug/ml|500ug/ml|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DY330|dy330|NN|_ -LRB-|-lrb-|-LRB-|_ W3110|w3110|NN|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP time|time|NN|_ point|point|NN|_ 8|8|CD|_
E.coli|e.coli|NN|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug/ml|500ug/ml|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_
Huiyi|Huiyi|NNP|_ ,|,|,|_ ,|,|,|_ Chen|Chen|NNP|_
The|The|NNP|_ .|.|.|_ align|align|VB|_ files|file|NNS|_ have|have|VBP|_ been|be|VBN|_ processed|process|VBN|_ using|use|VBG|_ tagalign|tagalign|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ first|first|JJ|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ extended|extend|VBN|_ to|to|TO|_ account|account|VB|_ for|for|IN|_ the|the|DT|_ linker|linker|NN|_ .|.|.|_
Clarified|clarify|VBD|_ extracts|extract|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ microccocal|microccocal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ purified|purify|VBN|_ through|through|IN|_ a|a|DT|_ sucrose|sucrose|NN|_ cushion|cushion|NN|_ ,|,|,|_ and|and|CC|_ affinity|affinity|NN|_ purified|purify|VBN|_ via|via|IN|_ TF|tf|NN|_ .|.|.|_ Ribosome-protected|ribosome-protected|JJ|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ Selective|selective|JJ|_ ribosome|ribosome|NN|_ profiling|profile|VBG|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ chloramphenicol|chloramphenicol|NN|_ pre-treatment|pre-treatment|NN|_ and|and|CC|_ centrifugation|centrifugation|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ chloramphenicol|chloramphenicol|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ with|with|IN|_ washed|wash|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X100|x100|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ NP-40|np-40|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ µl/ml|µl/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ ,|,|,|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ over|over|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ The|the|DT|_ frozen|frozen|JJ|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ MC4100|mc4100|NN|_ ∆|∆|NN|_ tig|tig|NN|GEN :|:|:|_ :|:|:|_ kan|kan|FW|_ pTig-TEV-Avi|ptig-tev-avi|FW|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ chloramphenicol|chloramphenicol|NN|_ pre-treatment|pre-treatment|NN|_ and|and|CC|_ centrifugation|centrifugation|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ chloramphenicol|chloramphenicol|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ with|with|IN|_ washed|wash|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X100|x100|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ NP-40|np-40|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ µl/ml|µl/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ ,|,|,|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ over|over|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ The|the|DT|_ frozen|frozen|JJ|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
Eugene|Eugene|NNP|_ ,|,|,|_ ,|,|,|_ Oh|oh|UH|_
The|the|DT|_ .|.|.|_ align|align|VB|_ files|file|NNS|_ have|have|VBP|_ been|be|VBN|_ processed|process|VBN|_ using|use|VBG|_ tagalign|tagalign|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ first|first|JJ|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ extended|extend|VBN|_ to|to|TO|_ account|account|VB|_ for|for|IN|_ the|the|DT|_ linker|linker|NN|_ .|.|.|_
Clarified|clarify|VBD|_ extracts|extract|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ microccocal|microccocal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ purified|purify|VBN|_ through|through|IN|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ .|.|.|_ Ribosome-protected|ribosome-protected|JJ|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ chloramphenicol|chloramphenicol|NN|_ pre-treatment|pre-treatment|NN|_ and|and|CC|_ centrifugation|centrifugation|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ chloramphenicol|chloramphenicol|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ with|with|IN|_ washed|wash|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X100|x100|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ NP-40|np-40|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ µl/ml|µl/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ ,|,|,|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ over|over|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ The|the|DT|_ frozen|frozen|JJ|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ MC4100|mc4100|NN|_ ∆|∆|NN|_ tig|tig|NN|GEN :|:|:|_ :|:|:|_ kan|kan|FW|_ pTig-TEV-Avi|ptig-tev-avi|FW|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ chloramphenicol|chloramphenicol|NN|_ pre-treatment|pre-treatment|NN|_ and|and|CC|_ centrifugation|centrifugation|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ chloramphenicol|chloramphenicol|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ with|with|IN|_ washed|wash|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X100|x100|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ NP-40|np-40|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ µl/ml|µl/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ ,|,|,|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ over|over|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ The|the|DT|_ frozen|frozen|JJ|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
Eugene|Eugene|NNP|_ ,|,|,|_ ,|,|,|_ Oh|oh|UH|_
The|the|DT|_ .|.|.|_ align|align|VB|_ files|file|NNS|_ have|have|VBP|_ been|be|VBN|_ processed|process|VBN|_ using|use|VBG|_ tagalign|tagalign|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ first|first|JJ|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ extended|extend|VBN|_ to|to|TO|_ account|account|VB|_ for|for|IN|_ the|the|DT|_ linker|linker|NN|_ .|.|.|_
Clarified|clarify|VBD|_ extracts|extract|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ microccocal|microccocal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ purified|purify|VBN|_ through|through|IN|_ a|a|DT|_ sucrose|sucrose|NN|_ cushion|cushion|NN|_ ,|,|,|_ and|and|CC|_ affinity|affinity|NN|_ purified|purify|VBN|_ via|via|IN|_ TF|tf|NN|_ .|.|.|_ Ribosome-protected|ribosome-protected|JJ|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ Selective|selective|JJ|_ ribosome|ribosome|NN|_ profiling|profile|VBG|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ chloramphenicol|chloramphenicol|NN|_ pre-treatment|pre-treatment|NN|_ and|and|CC|_ centrifugation|centrifugation|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ chloramphenicol|chloramphenicol|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ with|with|IN|_ washed|wash|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X100|x100|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ NP-40|np-40|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ µl/ml|µl/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ ,|,|,|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ over|over|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ The|the|DT|_ frozen|frozen|JJ|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ MC4100|mc4100|NN|_ ∆|∆|NN|_ tig|tig|NN|GEN :|:|:|_ :|:|:|_ kan|kan|FW|_ pTig-TEV-Avi|ptig-tev-avi|FW|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ chloramphenicol|chloramphenicol|NN|_ pre-treatment|pre-treatment|NN|_ and|and|CC|_ centrifugation|centrifugation|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ chloramphenicol|chloramphenicol|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ with|with|IN|_ washed|wash|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X100|x100|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ NP-40|np-40|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ µl/ml|µl/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ ,|,|,|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ over|over|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ The|the|DT|_ frozen|frozen|JJ|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
Eugene|Eugene|NNP|_ ,|,|,|_ ,|,|,|_ Oh|oh|UH|_
The|the|DT|_ .|.|.|_ align|align|VB|_ files|file|NNS|_ have|have|VBP|_ been|be|VBN|_ processed|process|VBN|_ using|use|VBG|_ tagalign|tagalign|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ first|first|JJ|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ extended|extend|VBN|_ to|to|TO|_ account|account|VB|_ for|for|IN|_ the|the|DT|_ linker|linker|NN|_ .|.|.|_
Clarified|clarify|VBD|_ extracts|extract|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ microccocal|microccocal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ purified|purify|VBN|_ through|through|IN|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ .|.|.|_ Ribosome-protected|ribosome-protected|JJ|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ chloramphenicol|chloramphenicol|NN|_ pre-treatment|pre-treatment|NN|_ and|and|CC|_ centrifugation|centrifugation|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ chloramphenicol|chloramphenicol|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ with|with|IN|_ washed|wash|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X100|x100|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ NP-40|np-40|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ µl/ml|µl/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ ,|,|,|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ over|over|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ The|the|DT|_ frozen|frozen|JJ|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ MC4100|mc4100|NN|_ ∆|∆|NN|_ tig|tig|NN|GEN :|:|:|_ :|:|:|_ kan|kan|FW|_ pTig-TEV-Avi|ptig-tev-avi|FW|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ chloramphenicol|chloramphenicol|NN|_ pre-treatment|pre-treatment|NN|_ and|and|CC|_ centrifugation|centrifugation|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ chloramphenicol|chloramphenicol|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ with|with|IN|_ washed|wash|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X100|x100|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ NP-40|np-40|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ µl/ml|µl/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ ,|,|,|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ over|over|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ The|the|DT|_ frozen|frozen|JJ|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
Eugene|Eugene|NNP|_ ,|,|,|_ ,|,|,|_ Oh|oh|UH|_
The|the|DT|_ .|.|.|_ align|align|VB|_ files|file|NNS|_ have|have|VBP|_ been|be|VBN|_ processed|process|VBN|_ using|use|VBG|_ tagalign|tagalign|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ first|first|JJ|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ extended|extend|VBN|_ to|to|TO|_ account|account|VB|_ for|for|IN|_ the|the|DT|_ linker|linker|NN|_ .|.|.|_
Clarified|clarify|VBD|_ extracts|extract|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ microccocal|microccocal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ purified|purify|VBN|_ through|through|IN|_ a|a|DT|_ sucrose|sucrose|NN|_ cushion|cushion|NN|_ ,|,|,|_ and|and|CC|_ affinity|affinity|NN|_ purified|purify|VBN|_ via|via|IN|_ TF|tf|NN|_ .|.|.|_ Ribosome-protected|ribosome-protected|JJ|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ Selective|selective|JJ|_ ribosome|ribosome|NN|_ profiling|profile|VBG|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ after|after|IN|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ MC4100|mc4100|NN|_ ∆|∆|NN|_ tig|tig|NN|GEN :|:|:|_ :|:|:|_ kan|kan|FW|_ pTig-TEV-Avi|ptig-tev-avi|FW|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ after|after|IN|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
Eugene|Eugene|NNP|_ ,|,|,|_ ,|,|,|_ Oh|oh|UH|_
The|the|DT|_ .|.|.|_ align|align|VB|_ files|file|NNS|_ have|have|VBP|_ been|be|VBN|_ processed|process|VBN|_ using|use|VBG|_ tagalign|tagalign|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ first|first|JJ|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ extended|extend|VBN|_ to|to|TO|_ account|account|VB|_ for|for|IN|_ the|the|DT|_ linker|linker|NN|_ .|.|.|_
Clarified|clarify|VBD|_ extracts|extract|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ microccocal|microccocal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ purified|purify|VBN|_ through|through|IN|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ .|.|.|_ Ribosome-protected|ribosome-protected|JJ|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ after|after|IN|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ MC4100|mc4100|NN|_ ∆|∆|NN|_ tig|tig|NN|GEN :|:|:|_ :|:|:|_ kan|kan|FW|_ pTig-TEV-Avi|ptig-tev-avi|FW|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ after|after|IN|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
Eugene|Eugene|NNP|_ ,|,|,|_ ,|,|,|_ Oh|oh|UH|_
The|the|DT|_ .|.|.|_ align|align|VB|_ files|file|NNS|_ have|have|VBP|_ been|be|VBN|_ processed|process|VBN|_ using|use|VBG|_ tagalign|tagalign|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ first|first|JJ|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ extended|extend|VBN|_ to|to|TO|_ account|account|VB|_ for|for|IN|_ the|the|DT|_ linker|linker|NN|_ .|.|.|_
Clarified|clarify|VBD|_ extracts|extract|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ microccocal|microccocal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ purified|purify|VBN|_ through|through|IN|_ a|a|DT|_ sucrose|sucrose|NN|_ cushion|cushion|NN|_ ,|,|,|_ and|and|CC|_ affinity|affinity|NN|_ purified|purify|VBN|_ via|via|IN|_ TF|tf|NN|_ .|.|.|_ Ribosome-protected|ribosome-protected|JJ|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ Selective|selective|JJ|_ ribosome|ribosome|NN|_ profiling|profile|VBG|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ EDC|edc|NN|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ after|after|IN|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 20|20|CD|_ mM|mm|NN|KWSUPP EDC|edc|NN|_ ,|,|,|_ pH|ph|NN|_ 5.8|5.8|CD|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 250|250|CD|_ mM|mm|NN|KWSUPP glycine|glycine|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.0|8.0|CD|_ ,|,|,|_ and|and|CC|_ 4|4|CD|_ mM|mm|NN|KWSUPP NaHCO3|nahco3|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ MC4100|mc4100|NN|_ ∆|∆|NN|_ tig|tig|NN|GEN :|:|:|_ :|:|:|_ kan|kan|FW|_ pTig-TEV-Avi|ptig-tev-avi|FW|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ EDC|edc|NN|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ after|after|IN|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 20|20|CD|_ mM|mm|NN|KWSUPP EDC|edc|NN|_ ,|,|,|_ pH|ph|NN|_ 5.8|5.8|CD|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 250|250|CD|_ mM|mm|NN|KWSUPP glycine|glycine|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.0|8.0|CD|_ ,|,|,|_ and|and|CC|_ 4|4|CD|_ mM|mm|NN|KWSUPP NaHCO3|nahco3|NN|_ .|.|.|_
Eugene|Eugene|NNP|_ ,|,|,|_ ,|,|,|_ Oh|oh|UH|_
The|the|DT|_ .|.|.|_ align|align|VB|_ files|file|NNS|_ have|have|VBP|_ been|be|VBN|_ processed|process|VBN|_ using|use|VBG|_ tagalign|tagalign|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ first|first|JJ|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ extended|extend|VBN|_ to|to|TO|_ account|account|VB|_ for|for|IN|_ the|the|DT|_ linker|linker|NN|_ .|.|.|_
Clarified|clarify|VBD|_ extracts|extract|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ microccocal|microccocal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ purified|purify|VBN|_ through|through|IN|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ .|.|.|_ Ribosome-protected|ribosome-protected|JJ|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ EDC|edc|NN|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ after|after|IN|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 20|20|CD|_ mM|mm|NN|KWSUPP EDC|edc|NN|_ ,|,|,|_ pH|ph|NN|_ 5.8|5.8|CD|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 250|250|CD|_ mM|mm|NN|KWSUPP glycine|glycine|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.0|8.0|CD|_ ,|,|,|_ and|and|CC|_ 4|4|CD|_ mM|mm|NN|KWSUPP NaHCO3|nahco3|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ MC4100|mc4100|NN|_ ∆|∆|NN|_ tig|tig|NN|GEN :|:|:|_ :|:|:|_ kan|kan|FW|_ pTig-TEV-Avi|ptig-tev-avi|FW|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg/ml|µg/ml|NN|_ of|of|IN|_ carbenicillin|carbenicillin|NN|_ ,|,|,|_ 40|40|CD|_ µg/ml|µg/ml|NN|_ biotin|biotin|NN|SUPP ,|,|,|_ and|and|CC|_ 70|70|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ back|back|JJ|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.45|0.45|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ EDC|edc|NN|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ after|after|IN|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 20|20|CD|_ mM|mm|NN|KWSUPP EDC|edc|NN|_ ,|,|,|_ pH|ph|NN|_ 5.8|5.8|CD|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 250|250|CD|_ mM|mm|NN|KWSUPP glycine|glycine|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.0|8.0|CD|_ ,|,|,|_ and|and|CC|_ 4|4|CD|_ mM|mm|NN|KWSUPP NaHCO3|nahco3|NN|_ .|.|.|_
Eugene|Eugene|NNP|_ ,|,|,|_ ,|,|,|_ Oh|oh|UH|_
Using|use|VBG|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ python|python|NN|_ -LRB-|-lrb-|-LRB-|_ 3.2.1|3.2.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ 0.12.7|0.12.7|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ sequencing|sequencing|NN|_ data|datum|NNS|_ ,|,|,|_ we|we|PRP|_ isolated|isolate|VBD|_ reads|read|VBZ|_ which|which|WDT|_ contained|contain|VBD|_ barcode|barcode|NN|_ sequences|sequence|NNS|_ that|that|WDT|_ corresponded|correspond|VBD|_ to|to|TO|_ our|we|PRP$|_ original|original|JJ|_ list|list|NN|_ of|of|IN|_ single|single|JJ|_ molecule|molecule|NN|_ barcodes|barcode|NNS|_ in|in|IN|_ both|both|CC|_ forward|forward|RB|_ and|and|CC|_ reverse|reverse|VB|_ reads|read|VBZ|_ for|for|IN|_ each|each|DT|_ sequence|sequence|NN|_ pair|pair|NN|_ that|that|WDT|_ had|have|VBD|_ at|at|IN|_ most|most|JJS|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ We|we|PRP|_ then|then|RB|_ aligned|align|VBD|_ the|the|DT|_ first|first|JJ|_ 28|28|CD|_ bases|basis|NNS|_ -LRB-|-lrb-|-LRB-|_ 26|26|CD|_ bases|basis|NNS|_ for|for|IN|_ the|the|DT|_ second|second|JJ|_ sequencing|sequencing|NN|_ run|run|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ targeted|target|VBN|_ sequence|sequence|NN|_ of|of|IN|_ both|both|CC|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ reads|read|VBZ|_ of|of|IN|_ each|each|DT|_ cluster|cluster|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ and|and|CC|_ kept|keep|VBD|_ the|the|DT|_ sequences|sequence|NNS|_ that|that|WDT|_ uniquely|uniquely|RB|_ align|align|VB|_ fewer|fewer|JJR|_ than|than|IN|_ three|three|CD|_ mismatches|mismatch|NNS|_ and|and|CC|_ where|where|WRB|_ the|the|DT|_ two|two|CD|_ reads|read|VBZ|_ did|do|VBD|_ not|not|RB|_ map|map|VB|GEN to|to|TO|_ the|the|DT|_ same|same|JJ|_ sense|sense|NN|_ or|or|CC|_ antisense|antisense|JJ|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_ We|we|PRP|_ used|use|VBD|_ a|a|DT|_ detailed|detailed|JJ|_ filtering|filter|VBG|_ process|process|NN|_ to|to|TO|_ determine|determine|VB|_ the|the|DT|_ identity|identity|NN|_ of|of|IN|_ closely-mapped|closely-mapped|JJ|_ reads|read|VBZ|_ .|.|.|_ Mapped|map|VBN|_ sequence|sequence|NN|_ fragments|fragment|NNS|_ with|with|IN|_ a|a|DT|_ length|length|NN|_ of|of|IN|_ at|at|IN|_ least|least|JJS|_ 1,000|1,000|CD|_ bases|basis|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_ All|all|DT|_ sequences|sequence|NNS|_ within|within|IN|_ the|the|DT|_ same|same|JJ|_ transcription|transcription|NN|_ unit|unit|NN|_ that|that|WDT|_ had|have|VBD|_ the|the|DT|_ same|same|JJ|_ unique|unique|JJ|_ tag|tag|NN|GEN were|be|VBD|_ analyzed|analyze|VBN|_ further|further|RB|_ .|.|.|_ We|we|PRP|_ determined|determine|VBD|_ that|that|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ sequence|sequence|NN|_ with|with|IN|_ the|the|DT|_ same|same|JJ|_ unique|unique|JJ|_ tag|tag|NN|GEN were|be|VBD|_ identical|identical|JJ|_ if|if|IN|_ the|the|DT|_ distance|distance|NN|_ between|between|IN|_ their|they|PRP$|_ center|center|NN|_ positions|position|NNS|_ was|be|VBD|_ less|less|JJR|_ than|than|IN|_ four|four|CD|_ base-pairs|base-pair|NNS|_ and|and|CC|_ if|if|IN|_ the|the|DT|_ difference|difference|NN|_ in|in|IN|_ length|length|NN|_ was|be|VBD|_ less|less|JJR|_ than|than|IN|_ 9|9|CD|_ base-pairs|base-pair|NNS|_ .|.|.|_ Then|then|RB|_ for|for|IN|_ each|each|DT|_ unique|unique|JJ|_ sequence|sequence|NN|_ ,|,|,|_ we|we|PRP|_ counted|count|VBD|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ unique|unique|JJ|_ barcode|barcode|NN|_ tags|tag|NNS|_ that|that|WDT|_ appeared|appear|VBD|_ to|to|TO|_ determine|determine|VB|_ the|the|DT|_ copy|copy|NN|_ number|number|NN|_ of|of|IN|_ each|each|DT|_ sequence|sequence|NN|_ and|and|CC|_ mapped|map|VBD|_ each|each|DT|_ of|of|IN|_ them|they|PRP|_ to|to|TO|_ genes|gene|NNS|_ .|.|.|_ We|we|PRP|_ include|include|VBP|_ indexed|index|VBN|_ genome|genome|NN|_ viewer|viewer|NN|_ files|file|NNS|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ sam|sam|NN|_ and|and|CC|_ .|.|.|_ sai|sai|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ both|both|DT|_ experiments|experiment|NNS|_ using|use|VBG|_ both|both|CC|_ the|the|DT|_ conventional|conventional|JJ|_ method|method|NN|_ and|and|CC|_ the|the|DT|_ digital|digital|JJ|_ method|method|NN|_ .|.|.|_
Genome|Genome|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ -LSB-|-lsb-|-LRB-|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Standard|Standard|NNP|_ Paired-End|Paired-End|NNP|_ Illumina|Illumina|NNP|_ Library|Library|NNP|_ Construction|Construction|NNP|_ Protocol|Protocol|NNP|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ modified|modify|VBN|_ adapters|adapter|NNS|_ containing|contain|VBG|_ optimized|optimize|VBN|_ 20|20|CD|_ bp|bp|NN|_ barcode|barcode|NN|_ sequences|sequence|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ original|original|JJ|_ paper|paper|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ barcoded|barcoded|JJ|_ adapters|adapter|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ with|with|IN|_ a|a|DT|_ 2x101|2x101|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ sequencing|sequencing|NN|_ run|run|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2x51|2x51|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ the|the|DT|_ second|second|JJ|_ -RRB-|-rrb-|-RRB-|_ base|base|NN|_ paired-end|paired-end|NN|_ reads|read|VBZ|_ in|in|IN|_ one|one|CD|_ lane|lane|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ -LSB-|-lsb-|-LRB-|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ The|the|DT|_ resulting|result|VBG|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 500-fold|500-fold|JJ|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 3.5|3.5|CD|_ hours|hour|NNS|_ such|such|JJ|_ that|that|IN|_ O.D.|O.D.|NNP|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ became|become|VBD|_ 0.30-0.35|0.30-0.35|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
RNA|rna|NN|_ from|from|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ a|a|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ using|use|VBG|_ Phenol|Phenol|NNP|_ Chloroform|Chloroform|NNP|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ conventional|conventional|JJ|_ Illumina|Illumina|NNP|_ protocol|protocol|NN|_ for|for|IN|_ mRNA|mrna|NN|_ Sequencing|sequencing|NN|_ Sample|Sample|NNP|_ Preparation|Preparation|NNP|_ was|be|VBD|_ applied|apply|VBN|_ with|with|IN|_ a|a|DT|_ few|few|JJ|_ modifications|modification|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ original|original|JJ|_ paper|paper|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
reference|reference|NN|_ genome|genome|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ ,|,|,|_ lambda|lambda|NN|_ -|-|:|_ ,|,|,|_ rph-1|rph-1|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ -LSB-|-lsb-|-LRB-|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ The|the|DT|_ resulting|result|VBG|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 500-fold|500-fold|JJ|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 3.5|3.5|CD|_ hours|hour|NNS|_ such|such|JJ|_ that|that|IN|_ O.D.|O.D.|NNP|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ became|become|VBD|_ 0.30-0.35|0.30-0.35|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
RNA|rna|NN|_ from|from|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ a|a|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ using|use|VBG|_ Phenol|Phenol|NNP|_ Chloroform|Chloroform|NNP|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ conventional|conventional|JJ|_ Illumina|Illumina|NNP|_ protocol|protocol|NN|_ for|for|IN|_ mRNA|mrna|NN|_ Sequencing|sequencing|NN|_ Sample|Sample|NNP|_ Preparation|Preparation|NNP|_ was|be|VBD|_ applied|apply|VBN|_ with|with|IN|_ a|a|DT|_ few|few|JJ|_ modifications|modification|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ original|original|JJ|_ paper|paper|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Tony|Tony|NNP|_ ,|,|,|_ Z|z|NN|_ ,|,|,|_ Jia|Jia|NNP|_
Using|use|VBG|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ python|python|NN|_ -LRB-|-lrb-|-LRB-|_ 3.2.1|3.2.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ 0.12.7|0.12.7|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ sequencing|sequencing|NN|_ data|datum|NNS|_ ,|,|,|_ we|we|PRP|_ isolated|isolate|VBD|_ reads|read|VBZ|_ which|which|WDT|_ contained|contain|VBD|_ barcode|barcode|NN|_ sequences|sequence|NNS|_ that|that|WDT|_ corresponded|correspond|VBD|_ to|to|TO|_ our|we|PRP$|_ original|original|JJ|_ list|list|NN|_ of|of|IN|_ single|single|JJ|_ molecule|molecule|NN|_ barcodes|barcode|NNS|_ in|in|IN|_ both|both|CC|_ forward|forward|RB|_ and|and|CC|_ reverse|reverse|VB|_ reads|read|VBZ|_ for|for|IN|_ each|each|DT|_ sequence|sequence|NN|_ pair|pair|NN|_ that|that|WDT|_ had|have|VBD|_ at|at|IN|_ most|most|JJS|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ We|we|PRP|_ then|then|RB|_ aligned|align|VBD|_ the|the|DT|_ first|first|JJ|_ 28|28|CD|_ bases|basis|NNS|_ -LRB-|-lrb-|-LRB-|_ 26|26|CD|_ bases|basis|NNS|_ for|for|IN|_ the|the|DT|_ second|second|JJ|_ sequencing|sequencing|NN|_ run|run|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ targeted|target|VBN|_ sequence|sequence|NN|_ of|of|IN|_ both|both|CC|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ reads|read|VBZ|_ of|of|IN|_ each|each|DT|_ cluster|cluster|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ and|and|CC|_ kept|keep|VBD|_ the|the|DT|_ sequences|sequence|NNS|_ that|that|WDT|_ uniquely|uniquely|RB|_ align|align|VB|_ fewer|fewer|JJR|_ than|than|IN|_ three|three|CD|_ mismatches|mismatch|NNS|_ and|and|CC|_ where|where|WRB|_ the|the|DT|_ two|two|CD|_ reads|read|VBZ|_ did|do|VBD|_ not|not|RB|_ map|map|VB|GEN to|to|TO|_ the|the|DT|_ same|same|JJ|_ sense|sense|NN|_ or|or|CC|_ antisense|antisense|JJ|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_ We|we|PRP|_ used|use|VBD|_ a|a|DT|_ detailed|detailed|JJ|_ filtering|filter|VBG|_ process|process|NN|_ to|to|TO|_ determine|determine|VB|_ the|the|DT|_ identity|identity|NN|_ of|of|IN|_ closely-mapped|closely-mapped|JJ|_ reads|read|VBZ|_ .|.|.|_ Mapped|map|VBN|_ sequence|sequence|NN|_ fragments|fragment|NNS|_ with|with|IN|_ a|a|DT|_ length|length|NN|_ of|of|IN|_ at|at|IN|_ least|least|JJS|_ 1,000|1,000|CD|_ bases|basis|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_ All|all|DT|_ sequences|sequence|NNS|_ within|within|IN|_ the|the|DT|_ same|same|JJ|_ transcription|transcription|NN|_ unit|unit|NN|_ that|that|WDT|_ had|have|VBD|_ the|the|DT|_ same|same|JJ|_ unique|unique|JJ|_ tag|tag|NN|GEN were|be|VBD|_ analyzed|analyze|VBN|_ further|further|RB|_ .|.|.|_ We|we|PRP|_ determined|determine|VBD|_ that|that|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ sequence|sequence|NN|_ with|with|IN|_ the|the|DT|_ same|same|JJ|_ unique|unique|JJ|_ tag|tag|NN|GEN were|be|VBD|_ identical|identical|JJ|_ if|if|IN|_ the|the|DT|_ distance|distance|NN|_ between|between|IN|_ their|they|PRP$|_ center|center|NN|_ positions|position|NNS|_ was|be|VBD|_ less|less|JJR|_ than|than|IN|_ four|four|CD|_ base-pairs|base-pair|NNS|_ and|and|CC|_ if|if|IN|_ the|the|DT|_ difference|difference|NN|_ in|in|IN|_ length|length|NN|_ was|be|VBD|_ less|less|JJR|_ than|than|IN|_ 9|9|CD|_ base-pairs|base-pair|NNS|_ .|.|.|_ Then|then|RB|_ for|for|IN|_ each|each|DT|_ unique|unique|JJ|_ sequence|sequence|NN|_ ,|,|,|_ we|we|PRP|_ counted|count|VBD|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ unique|unique|JJ|_ barcode|barcode|NN|_ tags|tag|NNS|_ that|that|WDT|_ appeared|appear|VBD|_ to|to|TO|_ determine|determine|VB|_ the|the|DT|_ copy|copy|NN|_ number|number|NN|_ of|of|IN|_ each|each|DT|_ sequence|sequence|NN|_ and|and|CC|_ mapped|map|VBD|_ each|each|DT|_ of|of|IN|_ them|they|PRP|_ to|to|TO|_ genes|gene|NNS|_ .|.|.|_ We|we|PRP|_ include|include|VBP|_ indexed|index|VBN|_ genome|genome|NN|_ viewer|viewer|NN|_ files|file|NNS|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ sam|sam|NN|_ and|and|CC|_ .|.|.|_ sai|sai|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ both|both|DT|_ experiments|experiment|NNS|_ using|use|VBG|_ both|both|CC|_ the|the|DT|_ conventional|conventional|JJ|_ method|method|NN|_ and|and|CC|_ the|the|DT|_ digital|digital|JJ|_ method|method|NN|_ .|.|.|_
Genome|Genome|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ -LSB-|-lsb-|-LRB-|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Standard|Standard|NNP|_ Paired-End|Paired-End|NNP|_ Illumina|Illumina|NNP|_ Library|Library|NNP|_ Construction|Construction|NNP|_ Protocol|Protocol|NNP|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ modified|modify|VBN|_ adapters|adapter|NNS|_ containing|contain|VBG|_ optimized|optimize|VBN|_ 20|20|CD|_ bp|bp|NN|_ barcode|barcode|NN|_ sequences|sequence|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ original|original|JJ|_ paper|paper|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ barcoded|barcoded|JJ|_ adapters|adapter|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ with|with|IN|_ a|a|DT|_ 2x101|2x101|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ sequencing|sequencing|NN|_ run|run|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2x51|2x51|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ the|the|DT|_ second|second|JJ|_ -RRB-|-rrb-|-RRB-|_ base|base|NN|_ paired-end|paired-end|NN|_ reads|read|VBZ|_ in|in|IN|_ one|one|CD|_ lane|lane|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ -LSB-|-lsb-|-LRB-|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ The|the|DT|_ resulting|result|VBG|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 500-fold|500-fold|JJ|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 3.5|3.5|CD|_ hours|hour|NNS|_ such|such|JJ|_ that|that|IN|_ O.D.|O.D.|NNP|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ became|become|VBD|_ 0.30-0.35|0.30-0.35|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
RNA|rna|NN|_ from|from|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ a|a|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ using|use|VBG|_ Phenol|Phenol|NNP|_ Chloroform|Chloroform|NNP|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ conventional|conventional|JJ|_ Illumina|Illumina|NNP|_ protocol|protocol|NN|_ for|for|IN|_ mRNA|mrna|NN|_ Sequencing|sequencing|NN|_ Sample|Sample|NNP|_ Preparation|Preparation|NNP|_ was|be|VBD|_ applied|apply|VBN|_ with|with|IN|_ a|a|DT|_ few|few|JJ|_ modifications|modification|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ original|original|JJ|_ paper|paper|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
reference|reference|NN|_ genome|genome|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ ,|,|,|_ lambda|lambda|NN|_ -|-|:|_ ,|,|,|_ rph-1|rph-1|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ -LSB-|-lsb-|-LRB-|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ The|the|DT|_ resulting|result|VBG|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 500-fold|500-fold|JJ|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 3.5|3.5|CD|_ hours|hour|NNS|_ such|such|JJ|_ that|that|IN|_ O.D.|O.D.|NNP|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ became|become|VBD|_ 0.30-0.35|0.30-0.35|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
RNA|rna|NN|_ from|from|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ a|a|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ using|use|VBG|_ Phenol|Phenol|NNP|_ Chloroform|Chloroform|NNP|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ conventional|conventional|JJ|_ Illumina|Illumina|NNP|_ protocol|protocol|NN|_ for|for|IN|_ mRNA|mrna|NN|_ Sequencing|sequencing|NN|_ Sample|Sample|NNP|_ Preparation|Preparation|NNP|_ was|be|VBD|_ applied|apply|VBN|_ with|with|IN|_ a|a|DT|_ few|few|JJ|_ modifications|modification|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ original|original|JJ|_ paper|paper|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Tony|Tony|NNP|_ ,|,|,|_ Z|z|NN|_ ,|,|,|_ Jia|Jia|NNP|_
cDNA|cdna|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ so|so|RB|_ that|that|IN|_ the|the|DT|_ quality|quality|NN|_ at|at|IN|_ each|each|DT|_ base|base|NN|_ position|position|NN|_ was|be|VBD|_ above|above|IN|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 15-20|15-20|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ mapped|map|VBD|_ either|either|CC|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ published|publish|VBN|_ genome|genome|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Genbank|Genbank|NNP|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ the|the|DT|_ pAR060302|par060302|NN|_ published|publish|VBN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Genbank|Genbank|NNP|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ NC|nc|NN|_ _|_|SYM|_ 092692|092692|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BOWTIE|BOWTIE|NNP|_ .|.|.|_ The|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ DH5α|dh5α|NN|_ has|have|VBZ|_ an|a|DT|_ incomplete|incomplete|JJ|_ annotation|annotation|NN|_ and|and|CC|_ for|for|IN|_ this|this|DT|_ reason|reason|NN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ annotation|annotation|NN|_ was|be|VBD|_ used|use|VBN|_ ,|,|,|_ representing|represent|VBG|_ an|a|DT|_ estimation|estimation|NN|_ of|of|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ due|due|JJ|_ to|to|TO|_ exposure|exposure|NN|_ of|of|IN|_ antimicrobials|antimicrobial|NNS|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ for|for|IN|_ 3|3|CD|_ seperate|seperate|JJ|_ sequencing|sequencing|NN|_ runs|run|NNS|_ were|be|VBD|_ combined|combine|VBN|_ because|because|IN|_ some|some|DT|_ sequencing|sequencing|NN|_ runs|run|NNS|_ were|be|VBD|_ not|not|RB|_ fully|fully|RB|_ completed|complete|VBN|_ due|due|JJ|_ to|to|TO|_ technical|technical|JJ|_ difficulties|difficulty|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ condition|condition|NN|_ ,|,|,|_ graphs|graph|NNS|_ representing|represent|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ were|be|VBD|_ generated|generate|VBN|_ and|and|CC|_ visualized|visualize|VBN|_ using|use|VBG|_ the|the|DT|_ Integrated|Integrated|NNP|_ Genome|Genome|NNP|_ Viewer|Viewer|NNP|_ -LRB-|-lrb-|-LRB-|_ IGV|igv|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Images|image|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ XplasMap|xplasmap|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.iayork.com/XPlasMap/|http://www.iayork.com/xplasmap/|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IGV|igv|NN|_ .|.|.|_ The|the|DT|_ reads|read|VBZ|_ mapped|map|VBN|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ gene|gene|NN|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ reads|read|VBZ|_ was|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ either|either|CC|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ chromosome|chromosome|NN|_ or|or|CC|_ the|the|DT|_ pAR060302|par060302|NN|_ annotation|annotation|NN|_ and|and|CC|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ global|global|JJ|_ normalization|normalization|NN|_ .|.|.|_ The|the|DT|_ per|per|IN|_ kilobase|kilobase|NN|_ cDNA|cdna|NN|_ length|length|NN|_ normalized|normalize|VBD|_ the|the|DT|_ effect|effect|NN|_ of|of|IN|_ different|different|JJ|_ length|length|NN|_ of|of|IN|_ cDNAs|cdna|NNS|_ such|such|JJ|_ that|that|IN|_ the|the|DT|_ sequence|sequence|NN|_ reads|read|VBZ|_ have|have|VB|_ a|a|DT|_ equal|equal|JJ|_ chance|chance|NN|_ to|to|TO|_ map|map|VB|GEN on|on|IN|_ the|the|DT|_ long|long|JJ|_ cDNA|cdna|NN|_ regions|region|NNS|_ and|and|CC|_ the|the|DT|_ short|short|JJ|_ cDNA|cdna|NN|_ regions|region|NNS|_ .|.|.|_ After|after|IN|_ RPKM|rpkm|NN|_ normalization|normalization|NN|_ ,|,|,|_ each|each|DT|_ sample|sample|NN|_ is|be|VBZ|_ comparable|comparable|JJ|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ .|.|.|_ An|a|DT|_ R|r|NN|_ package|package|NN|_ ,|,|,|_ DEGseq|degseq|NN|_ ,|,|,|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ identify|identify|VB|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ between|between|IN|_ the|the|DT|_ control|control|NN|_ and|and|CC|_ each|each|DT|_ antibiotic|antibiotic|JJ|_ treatment|treatment|NN|_ condition|condition|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ a|a|DT|_ DNase|dnase|NN|_ treatment|treatment|NN|_ to|to|TO|_ eliminate|eliminate|VB|_ DNA|dna|NN|_ contamination|contamination|NN|_ from|from|IN|_ the|the|DT|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ treatment|treatment|NN|_ was|be|VBD|_ also|also|RB|_ included|include|VBN|_ to|to|TO|_ deplete|deplete|VB|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ MicrobExpress|MicrobExpress|NNP|_ ,|,|,|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ growth|growth|NN|_ condition|condition|NN|_ were|be|VBD|_ pooled|pool|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ DH5α|dh5α|NN|_ harboring|harbor|VBG|_ pAR060302|par060302|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ DifcoTM|difcotm|NN|_ Luria-Bertani|luria-bertani|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ aliquots|aliquot|NNS|_ at|at|IN|_ 37º|37º|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.5|0.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH5α|dh5α|NN|_ -LRB-|-lrb-|-LRB-|_ pAR060302|par060302|NN|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ DH5α|dh5α|NN|_ harboring|harbor|VBG|_ pAR060302|par060302|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ DifcoTM|difcotm|NN|_ Luria-Bertani|luria-bertani|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ aliquots|aliquot|NNS|_ at|at|IN|_ 37º|37º|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.5|0.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_
Timothy|Timothy|NNP|_ ,|,|,|_ J.|J.|NNP|_ ,|,|,|_ Johnson|Johnson|NNP|_
cDNA|cdna|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ so|so|RB|_ that|that|IN|_ the|the|DT|_ quality|quality|NN|_ at|at|IN|_ each|each|DT|_ base|base|NN|_ position|position|NN|_ was|be|VBD|_ above|above|IN|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 15-20|15-20|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ mapped|map|VBD|_ either|either|CC|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ published|publish|VBN|_ genome|genome|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Genbank|Genbank|NNP|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ the|the|DT|_ pAR060302|par060302|NN|_ published|publish|VBN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Genbank|Genbank|NNP|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ NC|nc|NN|_ _|_|SYM|_ 092692|092692|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BOWTIE|BOWTIE|NNP|_ .|.|.|_ The|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ DH5α|dh5α|NN|_ has|have|VBZ|_ an|a|DT|_ incomplete|incomplete|JJ|_ annotation|annotation|NN|_ and|and|CC|_ for|for|IN|_ this|this|DT|_ reason|reason|NN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ annotation|annotation|NN|_ was|be|VBD|_ used|use|VBN|_ ,|,|,|_ representing|represent|VBG|_ an|a|DT|_ estimation|estimation|NN|_ of|of|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ due|due|JJ|_ to|to|TO|_ exposure|exposure|NN|_ of|of|IN|_ antimicrobials|antimicrobial|NNS|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ for|for|IN|_ 3|3|CD|_ seperate|seperate|JJ|_ sequencing|sequencing|NN|_ runs|run|NNS|_ were|be|VBD|_ combined|combine|VBN|_ because|because|IN|_ some|some|DT|_ sequencing|sequencing|NN|_ runs|run|NNS|_ were|be|VBD|_ not|not|RB|_ fully|fully|RB|_ completed|complete|VBN|_ due|due|JJ|_ to|to|TO|_ technical|technical|JJ|_ difficulties|difficulty|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ condition|condition|NN|_ ,|,|,|_ graphs|graph|NNS|_ representing|represent|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ were|be|VBD|_ generated|generate|VBN|_ and|and|CC|_ visualized|visualize|VBN|_ using|use|VBG|_ the|the|DT|_ Integrated|Integrated|NNP|_ Genome|Genome|NNP|_ Viewer|Viewer|NNP|_ -LRB-|-lrb-|-LRB-|_ IGV|igv|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Images|image|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ XplasMap|xplasmap|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.iayork.com/XPlasMap/|http://www.iayork.com/xplasmap/|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IGV|igv|NN|_ .|.|.|_ The|the|DT|_ reads|read|VBZ|_ mapped|map|VBN|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ gene|gene|NN|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ reads|read|VBZ|_ was|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ either|either|CC|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ chromosome|chromosome|NN|_ or|or|CC|_ the|the|DT|_ pAR060302|par060302|NN|_ annotation|annotation|NN|_ and|and|CC|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ global|global|JJ|_ normalization|normalization|NN|_ .|.|.|_ The|the|DT|_ per|per|IN|_ kilobase|kilobase|NN|_ cDNA|cdna|NN|_ length|length|NN|_ normalized|normalize|VBD|_ the|the|DT|_ effect|effect|NN|_ of|of|IN|_ different|different|JJ|_ length|length|NN|_ of|of|IN|_ cDNAs|cdna|NNS|_ such|such|JJ|_ that|that|IN|_ the|the|DT|_ sequence|sequence|NN|_ reads|read|VBZ|_ have|have|VB|_ a|a|DT|_ equal|equal|JJ|_ chance|chance|NN|_ to|to|TO|_ map|map|VB|GEN on|on|IN|_ the|the|DT|_ long|long|JJ|_ cDNA|cdna|NN|_ regions|region|NNS|_ and|and|CC|_ the|the|DT|_ short|short|JJ|_ cDNA|cdna|NN|_ regions|region|NNS|_ .|.|.|_ After|after|IN|_ RPKM|rpkm|NN|_ normalization|normalization|NN|_ ,|,|,|_ each|each|DT|_ sample|sample|NN|_ is|be|VBZ|_ comparable|comparable|JJ|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ .|.|.|_ An|a|DT|_ R|r|NN|_ package|package|NN|_ ,|,|,|_ DEGseq|degseq|NN|_ ,|,|,|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ identify|identify|VB|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ between|between|IN|_ the|the|DT|_ control|control|NN|_ and|and|CC|_ each|each|DT|_ antibiotic|antibiotic|JJ|_ treatment|treatment|NN|_ condition|condition|NN|_ .|.|.|_
Genome|Genome|NNP|_ Build|Build|NNP|_ :|:|:|_
Florfenicol|florfenicol|NN|_ _|_|NN|_ treatment|treatment|NN|_ _|_|NN|_ plasmidmappedreads|plasmidmappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012692.1|012692.1|CD|_
Flor|Flor|NNP|_ _|_|JJ|_ treatment|treatment|NN|_ _|_|NN|_ genomemappedreads|genomemappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ a|a|DT|_ DNase|dnase|NN|_ treatment|treatment|NN|_ to|to|TO|_ eliminate|eliminate|VB|_ DNA|dna|NN|_ contamination|contamination|NN|_ from|from|IN|_ the|the|DT|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ treatment|treatment|NN|_ was|be|VBD|_ also|also|RB|_ included|include|VBN|_ to|to|TO|_ deplete|deplete|VB|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ MicrobExpress|MicrobExpress|NNP|_ ,|,|,|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ growth|growth|NN|_ condition|condition|NN|_ were|be|VBD|_ pooled|pool|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ DH5α|dh5α|NN|_ harboring|harbor|VBG|_ pAR060302|par060302|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ DifcoTM|difcotm|NN|_ Luria-Bertani|luria-bertani|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ aliquots|aliquot|NNS|_ at|at|IN|_ 37º|37º|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.5|0.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_ with|with|IN|_ florfenicol|florfenicol|NN|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH5α|dh5α|NN|_ -LRB-|-lrb-|-LRB-|_ pAR060302|par060302|NN|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ florfenicol|florfenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ µg/mL|µg/ml|NN|_ final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ DH5α|dh5α|NN|_ harboring|harbor|VBG|_ pAR060302|par060302|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ DifcoTM|difcotm|NN|_ Luria-Bertani|luria-bertani|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ aliquots|aliquot|NNS|_ at|at|IN|_ 37º|37º|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.5|0.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_ with|with|IN|_ florfenicol|florfenicol|NN|_ treatment|treatment|NN|_
Timothy|Timothy|NNP|_ ,|,|,|_ J.|J.|NNP|_ ,|,|,|_ Johnson|Johnson|NNP|_
cDNA|cdna|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ so|so|RB|_ that|that|IN|_ the|the|DT|_ quality|quality|NN|_ at|at|IN|_ each|each|DT|_ base|base|NN|_ position|position|NN|_ was|be|VBD|_ above|above|IN|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 15-20|15-20|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ mapped|map|VBD|_ either|either|CC|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ published|publish|VBN|_ genome|genome|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Genbank|Genbank|NNP|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ the|the|DT|_ pAR060302|par060302|NN|_ published|publish|VBN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Genbank|Genbank|NNP|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ NC|nc|NN|_ _|_|SYM|_ 092692|092692|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BOWTIE|BOWTIE|NNP|_ .|.|.|_ The|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ DH5α|dh5α|NN|_ has|have|VBZ|_ an|a|DT|_ incomplete|incomplete|JJ|_ annotation|annotation|NN|_ and|and|CC|_ for|for|IN|_ this|this|DT|_ reason|reason|NN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ annotation|annotation|NN|_ was|be|VBD|_ used|use|VBN|_ ,|,|,|_ representing|represent|VBG|_ an|a|DT|_ estimation|estimation|NN|_ of|of|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ due|due|JJ|_ to|to|TO|_ exposure|exposure|NN|_ of|of|IN|_ antimicrobials|antimicrobial|NNS|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ for|for|IN|_ 3|3|CD|_ seperate|seperate|JJ|_ sequencing|sequencing|NN|_ runs|run|NNS|_ were|be|VBD|_ combined|combine|VBN|_ because|because|IN|_ some|some|DT|_ sequencing|sequencing|NN|_ runs|run|NNS|_ were|be|VBD|_ not|not|RB|_ fully|fully|RB|_ completed|complete|VBN|_ due|due|JJ|_ to|to|TO|_ technical|technical|JJ|_ difficulties|difficulty|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ condition|condition|NN|_ ,|,|,|_ graphs|graph|NNS|_ representing|represent|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ were|be|VBD|_ generated|generate|VBN|_ and|and|CC|_ visualized|visualize|VBN|_ using|use|VBG|_ the|the|DT|_ Integrated|Integrated|NNP|_ Genome|Genome|NNP|_ Viewer|Viewer|NNP|_ -LRB-|-lrb-|-LRB-|_ IGV|igv|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Images|image|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ XplasMap|xplasmap|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.iayork.com/XPlasMap/|http://www.iayork.com/xplasmap/|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IGV|igv|NN|_ .|.|.|_ The|the|DT|_ reads|read|VBZ|_ mapped|map|VBN|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ gene|gene|NN|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ reads|read|VBZ|_ was|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ either|either|CC|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ chromosome|chromosome|NN|_ or|or|CC|_ the|the|DT|_ pAR060302|par060302|NN|_ annotation|annotation|NN|_ and|and|CC|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ global|global|JJ|_ normalization|normalization|NN|_ .|.|.|_ The|the|DT|_ per|per|IN|_ kilobase|kilobase|NN|_ cDNA|cdna|NN|_ length|length|NN|_ normalized|normalize|VBD|_ the|the|DT|_ effect|effect|NN|_ of|of|IN|_ different|different|JJ|_ length|length|NN|_ of|of|IN|_ cDNAs|cdna|NNS|_ such|such|JJ|_ that|that|IN|_ the|the|DT|_ sequence|sequence|NN|_ reads|read|VBZ|_ have|have|VB|_ a|a|DT|_ equal|equal|JJ|_ chance|chance|NN|_ to|to|TO|_ map|map|VB|GEN on|on|IN|_ the|the|DT|_ long|long|JJ|_ cDNA|cdna|NN|_ regions|region|NNS|_ and|and|CC|_ the|the|DT|_ short|short|JJ|_ cDNA|cdna|NN|_ regions|region|NNS|_ .|.|.|_ After|after|IN|_ RPKM|rpkm|NN|_ normalization|normalization|NN|_ ,|,|,|_ each|each|DT|_ sample|sample|NN|_ is|be|VBZ|_ comparable|comparable|JJ|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ .|.|.|_ An|a|DT|_ R|r|NN|_ package|package|NN|_ ,|,|,|_ DEGseq|degseq|NN|_ ,|,|,|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ identify|identify|VB|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ between|between|IN|_ the|the|DT|_ control|control|NN|_ and|and|CC|_ each|each|DT|_ antibiotic|antibiotic|JJ|_ treatment|treatment|NN|_ condition|condition|NN|_ .|.|.|_
Genome|Genome|NNP|_ Build|Build|NNP|_ :|:|:|_
Ampicilin|Ampicilin|NNP|_ _|_|NN|_ treatment|treatment|NN|_ _|_|NN|_ plasmidmappedreads|plasmidmappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012692.1|012692.1|CD|_
Amp|Amp|NNP|_ _|_|NNP|_ Treatment|treatment|NN|_ _|_|NN|_ genomemappedreads|genomemappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ a|a|DT|_ DNase|dnase|NN|_ treatment|treatment|NN|_ to|to|TO|_ eliminate|eliminate|VB|_ DNA|dna|NN|_ contamination|contamination|NN|_ from|from|IN|_ the|the|DT|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ treatment|treatment|NN|_ was|be|VBD|_ also|also|RB|_ included|include|VBN|_ to|to|TO|_ deplete|deplete|VB|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ MicrobExpress|MicrobExpress|NNP|_ ,|,|,|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ growth|growth|NN|_ condition|condition|NN|_ were|be|VBD|_ pooled|pool|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ DH5α|dh5α|NN|_ harboring|harbor|VBG|_ pAR060302|par060302|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ DifcoTM|difcotm|NN|_ Luria-Bertani|luria-bertani|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ aliquots|aliquot|NNS|_ at|at|IN|_ 37º|37º|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.5|0.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_ with|with|IN|_ ampicilin|ampicilin|NN|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH5α|dh5α|NN|_ -LRB-|-lrb-|-LRB-|_ pAR060302|par060302|NN|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ DH5α|dh5α|NN|_ harboring|harbor|VBG|_ pAR060302|par060302|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ DifcoTM|difcotm|NN|_ Luria-Bertani|luria-bertani|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ aliquots|aliquot|NNS|_ at|at|IN|_ 37º|37º|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.5|0.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_ with|with|IN|_ ampicilin|ampicilin|NN|_ treatment|treatment|NN|_
Timothy|Timothy|NNP|_ ,|,|,|_ J.|J.|NNP|_ ,|,|,|_ Johnson|Johnson|NNP|_
cDNA|cdna|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ so|so|RB|_ that|that|IN|_ the|the|DT|_ quality|quality|NN|_ at|at|IN|_ each|each|DT|_ base|base|NN|_ position|position|NN|_ was|be|VBD|_ above|above|IN|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 15-20|15-20|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ mapped|map|VBD|_ either|either|CC|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ published|publish|VBN|_ genome|genome|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Genbank|Genbank|NNP|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ the|the|DT|_ pAR060302|par060302|NN|_ published|publish|VBN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Genbank|Genbank|NNP|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ NC|nc|NN|_ _|_|SYM|_ 092692|092692|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BOWTIE|BOWTIE|NNP|_ .|.|.|_ The|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ DH5α|dh5α|NN|_ has|have|VBZ|_ an|a|DT|_ incomplete|incomplete|JJ|_ annotation|annotation|NN|_ and|and|CC|_ for|for|IN|_ this|this|DT|_ reason|reason|NN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ annotation|annotation|NN|_ was|be|VBD|_ used|use|VBN|_ ,|,|,|_ representing|represent|VBG|_ an|a|DT|_ estimation|estimation|NN|_ of|of|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ due|due|JJ|_ to|to|TO|_ exposure|exposure|NN|_ of|of|IN|_ antimicrobials|antimicrobial|NNS|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ for|for|IN|_ 3|3|CD|_ seperate|seperate|JJ|_ sequencing|sequencing|NN|_ runs|run|NNS|_ were|be|VBD|_ combined|combine|VBN|_ because|because|IN|_ some|some|DT|_ sequencing|sequencing|NN|_ runs|run|NNS|_ were|be|VBD|_ not|not|RB|_ fully|fully|RB|_ completed|complete|VBN|_ due|due|JJ|_ to|to|TO|_ technical|technical|JJ|_ difficulties|difficulty|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ condition|condition|NN|_ ,|,|,|_ graphs|graph|NNS|_ representing|represent|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ were|be|VBD|_ generated|generate|VBN|_ and|and|CC|_ visualized|visualize|VBN|_ using|use|VBG|_ the|the|DT|_ Integrated|Integrated|NNP|_ Genome|Genome|NNP|_ Viewer|Viewer|NNP|_ -LRB-|-lrb-|-LRB-|_ IGV|igv|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Images|image|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ XplasMap|xplasmap|NN|_ -LRB-|-lrb-|-LRB-|_ http://www.iayork.com/XPlasMap/|http://www.iayork.com/xplasmap/|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IGV|igv|NN|_ .|.|.|_ The|the|DT|_ reads|read|VBZ|_ mapped|map|VBN|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ gene|gene|NN|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ reads|read|VBZ|_ was|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ either|either|CC|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ chromosome|chromosome|NN|_ or|or|CC|_ the|the|DT|_ pAR060302|par060302|NN|_ annotation|annotation|NN|_ and|and|CC|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ global|global|JJ|_ normalization|normalization|NN|_ .|.|.|_ The|the|DT|_ per|per|IN|_ kilobase|kilobase|NN|_ cDNA|cdna|NN|_ length|length|NN|_ normalized|normalize|VBD|_ the|the|DT|_ effect|effect|NN|_ of|of|IN|_ different|different|JJ|_ length|length|NN|_ of|of|IN|_ cDNAs|cdna|NNS|_ such|such|JJ|_ that|that|IN|_ the|the|DT|_ sequence|sequence|NN|_ reads|read|VBZ|_ have|have|VB|_ a|a|DT|_ equal|equal|JJ|_ chance|chance|NN|_ to|to|TO|_ map|map|VB|GEN on|on|IN|_ the|the|DT|_ long|long|JJ|_ cDNA|cdna|NN|_ regions|region|NNS|_ and|and|CC|_ the|the|DT|_ short|short|JJ|_ cDNA|cdna|NN|_ regions|region|NNS|_ .|.|.|_ After|after|IN|_ RPKM|rpkm|NN|_ normalization|normalization|NN|_ ,|,|,|_ each|each|DT|_ sample|sample|NN|_ is|be|VBZ|_ comparable|comparable|JJ|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ .|.|.|_ An|a|DT|_ R|r|NN|_ package|package|NN|_ ,|,|,|_ DEGseq|degseq|NN|_ ,|,|,|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ identify|identify|VB|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ between|between|IN|_ the|the|DT|_ control|control|NN|_ and|and|CC|_ each|each|DT|_ antibiotic|antibiotic|JJ|_ treatment|treatment|NN|_ condition|condition|NN|_ .|.|.|_
Genome|Genome|NNP|_ Build|Build|NNP|_ :|:|:|_
Streptomycin|Streptomycin|NNP|_ _|_|NN|_ treatment|treatment|NN|_ _|_|NN|_ plasmidmappedreads|plasmidmappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 012692.1|012692.1|CD|_
Strep|strep|JJ|_ _|_|NN|_ treatment|treatment|NN|_ _|_|NN|_ genomemappedreads|genomemappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ a|a|DT|_ DNase|dnase|NN|_ treatment|treatment|NN|_ to|to|TO|_ eliminate|eliminate|VB|_ DNA|dna|NN|_ contamination|contamination|NN|_ from|from|IN|_ the|the|DT|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ treatment|treatment|NN|_ was|be|VBD|_ also|also|RB|_ included|include|VBN|_ to|to|TO|_ deplete|deplete|VB|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ MicrobExpress|MicrobExpress|NNP|_ ,|,|,|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ growth|growth|NN|_ condition|condition|NN|_ were|be|VBD|_ pooled|pool|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ DH5α|dh5α|NN|_ harboring|harbor|VBG|_ pAR060302|par060302|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ DifcoTM|difcotm|NN|_ Luria-Bertani|luria-bertani|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ aliquots|aliquot|NNS|_ at|at|IN|_ 37º|37º|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.5|0.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_ with|with|IN|_ streptomycin|streptomycin|NN|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH5α|dh5α|NN|_ -LRB-|-lrb-|-LRB-|_ pAR060302|par060302|NN|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ streptomycin|streptomycin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ DH5α|dh5α|NN|_ harboring|harbor|VBG|_ pAR060302|par060302|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ DifcoTM|difcotm|NN|_ Luria-Bertani|luria-bertani|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ aliquots|aliquot|NNS|_ at|at|IN|_ 37º|37º|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.5|0.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_ with|with|IN|_ streptomycin|streptomycin|NN|_ treatment|treatment|NN|_
Timothy|Timothy|NNP|_ ,|,|,|_ J.|J.|NNP|_ ,|,|,|_ Johnson|Johnson|NNP|_
Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ reads|read|VBZ|_ were|be|VBD|_ filtered|filter|VBN|_ by|by|IN|_ SGA|SGA|NNP|_ version|version|NN|_ 0.9.9|0.9.9|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ sga|sga|NN|_ preprocess|preprocess|NN|_ -|-|:|_ q|q|NN|_ 10|10|CD|_ -|-|:|_ f|f|LS|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ 25|25|CD|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ trim|trim|JJ|_ 10|10|CD|_ ,|,|,|_ quality|quality|NN|_ filter|filter|NN|_ 10|10|CD|_ ,|,|,|_ minimal|minimal|JJ|_ length|length|NN|_ 25|25|CD|_ -RRB-|-rrb-|-RRB-|_
preprocessed|preprocessed|JJ|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ BWA|BWA|NNP|_ toolkit|toolkit|NN|_ version|version|NN|_ 0.5.9-r16|0.5.9-r16|NN|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ bwa|bwa|NN|_ aln|aln|NN|_ -|-|:|_ q|q|NN|_ 20|20|CD|_
Differentially|differentially|RB|_ expressed|express|VBD|_ genes|gene|NNS|_ were|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ processing|process|VBG|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ with|with|IN|_ edgeR|edger|NN|_ R|r|NN|_ library|library|NN|_ version|version|NN|_ 2.6.9|2.6.9|CD|_ .|.|.|_ Normalized|normalize|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ were|be|VBD|_ averaged|average|VBN|_ between|between|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ .|.|.|_
Differentially|differentially|RB|_ expressed|express|VBD|_ -LRB-|-lrb-|-LRB-|_ DE|de|NN|_ -RRB-|-rrb-|-RRB-|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ stress|stress|NN|_ evolved|evolve|VBD|_ strains|strain|NNS|_ were|be|VBD|_ found|find|VBN|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ expression|expression|NN|_ levels|level|NNS|_ in|in|IN|_ the|the|DT|_ reference|reference|NN|_ G500|g500|NN|_ strain|strain|NN|_ using|use|VBG|_ the|the|DT|_ edgeR|edger|NN|_ R|r|NN|_ package|package|NN|_ .|.|.|_
Genes|gene|NNS|_ with|with|IN|_ BH|bh|NN|_ -LRB-|-lrb-|-LRB-|_ Benjamini|Benjamini|NNP|_ and|and|CC|_ Hochberg|Hochberg|NNP|_ -RRB-|-rrb-|-RRB-|_ adjusted|adjust|VBN|_ p-values|p-value|NNS|_ below|below|IN|_ 0.05|0.05|CD|_ threshold|threshold|NN|_ were|be|VBD|_ selected|select|VBN|_ as|as|IN|_ DE|de|NN|_ genes|gene|NNS|_ .|.|.|_
Genes|gene|NNS|_ from|from|IN|_ the|the|DT|_ amplified|amplify|VBN|_ regions|region|NNS|_ in|in|IN|_ O500|o500|NN|_ -LRB-|-lrb-|-LRB-|_ 12-fold|12-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ P500|p500|NN|_ -LRB-|-lrb-|-LRB-|_ two-fold|two-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ strains|strain|NNS|_ are|be|VBP|_ significantly|significantly|RB|_ over-expressed|over-expressed|JJ|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ :|:|:|_ average|average|JJ|_ log|log|NN|_ Fold|Fold|NNP|_ Change|Change|NNP|_ for|for|IN|_ concentrations|concentration|NNS|_ is|be|VBZ|_ +3.6|+3.6|CD|_ and|and|CC|_ +0.8|+0.8|CD|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ with|with|IN|_ p-values|p-values|NN|_ <|<|JJR|_ 10-20|10-20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ file|file|NN|_ ;|;|:|_ includes|include|VBZ|_ :|:|:|_ gene|gene|NN|_ differential|differential|JJ|_ expression|expression|NN|_ levels|level|NNS|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ G500|g500|NN|_ strain|strain|NN|_ with|with|IN|_ corresponding|corresponding|JJ|_ p-values|p-value|NNS|_ and|and|CC|_ processed|process|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ normolized|normolized|NN|_ and|and|CC|_ averaged|average|VBD|_ between|between|IN|_ 2|2|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Linked|link|VBN|_ as|as|IN|_ supplementary|supplementary|JJ|_ file|file|NN|_ on|on|IN|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ 1st|1st|JJ|_ and|and|CC|_ 2nd|2nd|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ linker|linker|NN|_ ligation|ligation|NN|_ and|and|CC|_ size|size|NN|_ selection|selection|NN|_ subjected|subject|VBN|_ to|to|TO|_ shotgun|shotgun|NN|_ sequencing|sequencing|NN|_ using|use|VBG|_ single|single|JJ|_ read|read|NN|_ 40bp|40bp|JJ|_ read|read|NN|_ length|length|NN|_ runs|run|VBZ|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ GAII|GAII|NNP|_ .|.|.|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG|mg|NN|_ 1655|1655|CD|_
stress|stress|NN|_ :|:|:|_ Minimal|minimal|JJ|_ medium|medium|NN|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
technical|technical|JJ|_ replicates|replicate|VBZ|_ :|:|:|_ 2|2|CD|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
Vadim|Vadim|NNP|_ ,|,|,|_ ,|,|,|_ Mozhayskiy|Mozhayskiy|NNP|_
Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ reads|read|VBZ|_ were|be|VBD|_ filtered|filter|VBN|_ by|by|IN|_ SGA|SGA|NNP|_ version|version|NN|_ 0.9.9|0.9.9|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ sga|sga|NN|_ preprocess|preprocess|NN|_ -|-|:|_ q|q|NN|_ 10|10|CD|_ -|-|:|_ f|f|LS|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ 25|25|CD|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ trim|trim|JJ|_ 10|10|CD|_ ,|,|,|_ quality|quality|NN|_ filter|filter|NN|_ 10|10|CD|_ ,|,|,|_ minimal|minimal|JJ|_ length|length|NN|_ 25|25|CD|_ -RRB-|-rrb-|-RRB-|_
preprocessed|preprocessed|JJ|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ BWA|BWA|NNP|_ toolkit|toolkit|NN|_ version|version|NN|_ 0.5.9-r16|0.5.9-r16|NN|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ bwa|bwa|NN|_ aln|aln|NN|_ -|-|:|_ q|q|NN|_ 20|20|CD|_
Differentially|differentially|RB|_ expressed|express|VBD|_ genes|gene|NNS|_ were|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ processing|process|VBG|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ with|with|IN|_ edgeR|edger|NN|_ R|r|NN|_ library|library|NN|_ version|version|NN|_ 2.6.9|2.6.9|CD|_ .|.|.|_ Normalized|normalize|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ were|be|VBD|_ averaged|average|VBN|_ between|between|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ .|.|.|_
Differentially|differentially|RB|_ expressed|express|VBD|_ -LRB-|-lrb-|-LRB-|_ DE|de|NN|_ -RRB-|-rrb-|-RRB-|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ stress|stress|NN|_ evolved|evolve|VBD|_ strains|strain|NNS|_ were|be|VBD|_ found|find|VBN|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ expression|expression|NN|_ levels|level|NNS|_ in|in|IN|_ the|the|DT|_ reference|reference|NN|_ G500|g500|NN|_ strain|strain|NN|_ using|use|VBG|_ the|the|DT|_ edgeR|edger|NN|_ R|r|NN|_ package|package|NN|_ .|.|.|_
Genes|gene|NNS|_ with|with|IN|_ BH|bh|NN|_ -LRB-|-lrb-|-LRB-|_ Benjamini|Benjamini|NNP|_ and|and|CC|_ Hochberg|Hochberg|NNP|_ -RRB-|-rrb-|-RRB-|_ adjusted|adjust|VBN|_ p-values|p-value|NNS|_ below|below|IN|_ 0.05|0.05|CD|_ threshold|threshold|NN|_ were|be|VBD|_ selected|select|VBN|_ as|as|IN|_ DE|de|NN|_ genes|gene|NNS|_ .|.|.|_
Genes|gene|NNS|_ from|from|IN|_ the|the|DT|_ amplified|amplify|VBN|_ regions|region|NNS|_ in|in|IN|_ O500|o500|NN|_ -LRB-|-lrb-|-LRB-|_ 12-fold|12-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ P500|p500|NN|_ -LRB-|-lrb-|-LRB-|_ two-fold|two-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ strains|strain|NNS|_ are|be|VBP|_ significantly|significantly|RB|_ over-expressed|over-expressed|JJ|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ :|:|:|_ average|average|JJ|_ log|log|NN|_ Fold|Fold|NNP|_ Change|Change|NNP|_ for|for|IN|_ concentrations|concentration|NNS|_ is|be|VBZ|_ +3.6|+3.6|CD|_ and|and|CC|_ +0.8|+0.8|CD|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ with|with|IN|_ p-values|p-values|NN|_ <|<|JJR|_ 10-20|10-20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ file|file|NN|_ ;|;|:|_ includes|include|VBZ|_ :|:|:|_ gene|gene|NN|_ differential|differential|JJ|_ expression|expression|NN|_ levels|level|NNS|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ G500|g500|NN|_ strain|strain|NN|_ with|with|IN|_ corresponding|corresponding|JJ|_ p-values|p-value|NNS|_ and|and|CC|_ processed|process|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ normolized|normolized|NN|_ and|and|CC|_ averaged|average|VBD|_ between|between|IN|_ 2|2|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Linked|link|VBN|_ as|as|IN|_ supplementary|supplementary|JJ|_ file|file|NN|_ on|on|IN|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ 1st|1st|JJ|_ and|and|CC|_ 2nd|2nd|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ linker|linker|NN|_ ligation|ligation|NN|_ and|and|CC|_ size|size|NN|_ selection|selection|NN|_ subjected|subject|VBN|_ to|to|TO|_ shotgun|shotgun|NN|_ sequencing|sequencing|NN|_ using|use|VBG|_ single|single|JJ|_ read|read|NN|_ 40bp|40bp|JJ|_ read|read|NN|_ length|length|NN|_ runs|run|VBZ|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ GAII|GAII|NNP|_ .|.|.|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG|mg|NN|_ 1655|1655|CD|_
stress|stress|NN|_ :|:|:|_ n-butanol|n-butanol|NN|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
technical|technical|JJ|_ replicates|replicate|VBZ|_ :|:|:|_ 2|2|CD|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
Vadim|Vadim|NNP|_ ,|,|,|_ ,|,|,|_ Mozhayskiy|Mozhayskiy|NNP|_
Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ reads|read|VBZ|_ were|be|VBD|_ filtered|filter|VBN|_ by|by|IN|_ SGA|SGA|NNP|_ version|version|NN|_ 0.9.9|0.9.9|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ sga|sga|NN|_ preprocess|preprocess|NN|_ -|-|:|_ q|q|NN|_ 10|10|CD|_ -|-|:|_ f|f|LS|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ 25|25|CD|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ trim|trim|JJ|_ 10|10|CD|_ ,|,|,|_ quality|quality|NN|_ filter|filter|NN|_ 10|10|CD|_ ,|,|,|_ minimal|minimal|JJ|_ length|length|NN|_ 25|25|CD|_ -RRB-|-rrb-|-RRB-|_
preprocessed|preprocessed|JJ|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ BWA|BWA|NNP|_ toolkit|toolkit|NN|_ version|version|NN|_ 0.5.9-r16|0.5.9-r16|NN|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ bwa|bwa|NN|_ aln|aln|NN|_ -|-|:|_ q|q|NN|_ 20|20|CD|_
Differentially|differentially|RB|_ expressed|express|VBD|_ genes|gene|NNS|_ were|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ processing|process|VBG|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ with|with|IN|_ edgeR|edger|NN|_ R|r|NN|_ library|library|NN|_ version|version|NN|_ 2.6.9|2.6.9|CD|_ .|.|.|_ Normalized|normalize|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ were|be|VBD|_ averaged|average|VBN|_ between|between|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ .|.|.|_
Differentially|differentially|RB|_ expressed|express|VBD|_ -LRB-|-lrb-|-LRB-|_ DE|de|NN|_ -RRB-|-rrb-|-RRB-|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ stress|stress|NN|_ evolved|evolve|VBD|_ strains|strain|NNS|_ were|be|VBD|_ found|find|VBN|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ expression|expression|NN|_ levels|level|NNS|_ in|in|IN|_ the|the|DT|_ reference|reference|NN|_ G500|g500|NN|_ strain|strain|NN|_ using|use|VBG|_ the|the|DT|_ edgeR|edger|NN|_ R|r|NN|_ package|package|NN|_ .|.|.|_
Genes|gene|NNS|_ with|with|IN|_ BH|bh|NN|_ -LRB-|-lrb-|-LRB-|_ Benjamini|Benjamini|NNP|_ and|and|CC|_ Hochberg|Hochberg|NNP|_ -RRB-|-rrb-|-RRB-|_ adjusted|adjust|VBN|_ p-values|p-value|NNS|_ below|below|IN|_ 0.05|0.05|CD|_ threshold|threshold|NN|_ were|be|VBD|_ selected|select|VBN|_ as|as|IN|_ DE|de|NN|_ genes|gene|NNS|_ .|.|.|_
Genes|gene|NNS|_ from|from|IN|_ the|the|DT|_ amplified|amplify|VBN|_ regions|region|NNS|_ in|in|IN|_ O500|o500|NN|_ -LRB-|-lrb-|-LRB-|_ 12-fold|12-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ P500|p500|NN|_ -LRB-|-lrb-|-LRB-|_ two-fold|two-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ strains|strain|NNS|_ are|be|VBP|_ significantly|significantly|RB|_ over-expressed|over-expressed|JJ|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ :|:|:|_ average|average|JJ|_ log|log|NN|_ Fold|Fold|NNP|_ Change|Change|NNP|_ for|for|IN|_ concentrations|concentration|NNS|_ is|be|VBZ|_ +3.6|+3.6|CD|_ and|and|CC|_ +0.8|+0.8|CD|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ with|with|IN|_ p-values|p-values|NN|_ <|<|JJR|_ 10-20|10-20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ file|file|NN|_ ;|;|:|_ includes|include|VBZ|_ :|:|:|_ gene|gene|NN|_ differential|differential|JJ|_ expression|expression|NN|_ levels|level|NNS|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ G500|g500|NN|_ strain|strain|NN|_ with|with|IN|_ corresponding|corresponding|JJ|_ p-values|p-value|NNS|_ and|and|CC|_ processed|process|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ normolized|normolized|NN|_ and|and|CC|_ averaged|average|VBD|_ between|between|IN|_ 2|2|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Linked|link|VBN|_ as|as|IN|_ supplementary|supplementary|JJ|_ file|file|NN|_ on|on|IN|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ 1st|1st|JJ|_ and|and|CC|_ 2nd|2nd|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ linker|linker|NN|_ ligation|ligation|NN|_ and|and|CC|_ size|size|NN|_ selection|selection|NN|_ subjected|subject|VBN|_ to|to|TO|_ shotgun|shotgun|NN|_ sequencing|sequencing|NN|_ using|use|VBG|_ single|single|JJ|_ read|read|NN|_ 40bp|40bp|JJ|_ read|read|NN|_ length|length|NN|_ runs|run|VBZ|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ GAII|GAII|NNP|_ .|.|.|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG|mg|NN|_ 1655|1655|CD|_
stress|stress|NN|_ :|:|:|_ oxidative|oxidative|JJ|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
technical|technical|JJ|_ replicates|replicate|VBZ|_ :|:|:|_ 2|2|CD|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
Vadim|Vadim|NNP|_ ,|,|,|_ ,|,|,|_ Mozhayskiy|Mozhayskiy|NNP|_
Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ reads|read|VBZ|_ were|be|VBD|_ filtered|filter|VBN|_ by|by|IN|_ SGA|SGA|NNP|_ version|version|NN|_ 0.9.9|0.9.9|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ sga|sga|NN|_ preprocess|preprocess|NN|_ -|-|:|_ q|q|NN|_ 10|10|CD|_ -|-|:|_ f|f|LS|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ 25|25|CD|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ trim|trim|JJ|_ 10|10|CD|_ ,|,|,|_ quality|quality|NN|_ filter|filter|NN|_ 10|10|CD|_ ,|,|,|_ minimal|minimal|JJ|_ length|length|NN|_ 25|25|CD|_ -RRB-|-rrb-|-RRB-|_
preprocessed|preprocessed|JJ|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ BWA|BWA|NNP|_ toolkit|toolkit|NN|_ version|version|NN|_ 0.5.9-r16|0.5.9-r16|NN|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ bwa|bwa|NN|_ aln|aln|NN|_ -|-|:|_ q|q|NN|_ 20|20|CD|_
Differentially|differentially|RB|_ expressed|express|VBD|_ genes|gene|NNS|_ were|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ processing|process|VBG|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ with|with|IN|_ edgeR|edger|NN|_ R|r|NN|_ library|library|NN|_ version|version|NN|_ 2.6.9|2.6.9|CD|_ .|.|.|_ Normalized|normalize|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ were|be|VBD|_ averaged|average|VBN|_ between|between|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ .|.|.|_
Differentially|differentially|RB|_ expressed|express|VBD|_ -LRB-|-lrb-|-LRB-|_ DE|de|NN|_ -RRB-|-rrb-|-RRB-|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ stress|stress|NN|_ evolved|evolve|VBD|_ strains|strain|NNS|_ were|be|VBD|_ found|find|VBN|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ expression|expression|NN|_ levels|level|NNS|_ in|in|IN|_ the|the|DT|_ reference|reference|NN|_ G500|g500|NN|_ strain|strain|NN|_ using|use|VBG|_ the|the|DT|_ edgeR|edger|NN|_ R|r|NN|_ package|package|NN|_ .|.|.|_
Genes|gene|NNS|_ with|with|IN|_ BH|bh|NN|_ -LRB-|-lrb-|-LRB-|_ Benjamini|Benjamini|NNP|_ and|and|CC|_ Hochberg|Hochberg|NNP|_ -RRB-|-rrb-|-RRB-|_ adjusted|adjust|VBN|_ p-values|p-value|NNS|_ below|below|IN|_ 0.05|0.05|CD|_ threshold|threshold|NN|_ were|be|VBD|_ selected|select|VBN|_ as|as|IN|_ DE|de|NN|_ genes|gene|NNS|_ .|.|.|_
Genes|gene|NNS|_ from|from|IN|_ the|the|DT|_ amplified|amplify|VBN|_ regions|region|NNS|_ in|in|IN|_ O500|o500|NN|_ -LRB-|-lrb-|-LRB-|_ 12-fold|12-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ P500|p500|NN|_ -LRB-|-lrb-|-LRB-|_ two-fold|two-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ strains|strain|NNS|_ are|be|VBP|_ significantly|significantly|RB|_ over-expressed|over-expressed|JJ|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ :|:|:|_ average|average|JJ|_ log|log|NN|_ Fold|Fold|NNP|_ Change|Change|NNP|_ for|for|IN|_ concentrations|concentration|NNS|_ is|be|VBZ|_ +3.6|+3.6|CD|_ and|and|CC|_ +0.8|+0.8|CD|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ with|with|IN|_ p-values|p-values|NN|_ <|<|JJR|_ 10-20|10-20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ file|file|NN|_ ;|;|:|_ includes|include|VBZ|_ :|:|:|_ gene|gene|NN|_ differential|differential|JJ|_ expression|expression|NN|_ levels|level|NNS|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ G500|g500|NN|_ strain|strain|NN|_ with|with|IN|_ corresponding|corresponding|JJ|_ p-values|p-value|NNS|_ and|and|CC|_ processed|process|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ normolized|normolized|NN|_ and|and|CC|_ averaged|average|VBD|_ between|between|IN|_ 2|2|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Linked|link|VBN|_ as|as|IN|_ supplementary|supplementary|JJ|_ file|file|NN|_ on|on|IN|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ 1st|1st|JJ|_ and|and|CC|_ 2nd|2nd|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ linker|linker|NN|_ ligation|ligation|NN|_ and|and|CC|_ size|size|NN|_ selection|selection|NN|_ subjected|subject|VBN|_ to|to|TO|_ shotgun|shotgun|NN|_ sequencing|sequencing|NN|_ using|use|VBG|_ single|single|JJ|_ read|read|NN|_ 40bp|40bp|JJ|_ read|read|NN|_ length|length|NN|_ runs|run|VBZ|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ GAII|GAII|NNP|_ .|.|.|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG|mg|NN|_ 1655|1655|CD|_
stress|stress|NN|_ :|:|:|_ osmotic|osmotic|JJ|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
technical|technical|JJ|_ replicates|replicate|VBZ|_ :|:|:|_ 2|2|CD|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
Vadim|Vadim|NNP|_ ,|,|,|_ ,|,|,|_ Mozhayskiy|Mozhayskiy|NNP|_
Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ reads|read|VBZ|_ were|be|VBD|_ filtered|filter|VBN|_ by|by|IN|_ SGA|SGA|NNP|_ version|version|NN|_ 0.9.9|0.9.9|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ sga|sga|NN|_ preprocess|preprocess|NN|_ -|-|:|_ q|q|NN|_ 10|10|CD|_ -|-|:|_ f|f|LS|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ 25|25|CD|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ trim|trim|JJ|_ 10|10|CD|_ ,|,|,|_ quality|quality|NN|_ filter|filter|NN|_ 10|10|CD|_ ,|,|,|_ minimal|minimal|JJ|_ length|length|NN|_ 25|25|CD|_ -RRB-|-rrb-|-RRB-|_
preprocessed|preprocessed|JJ|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ BWA|BWA|NNP|_ toolkit|toolkit|NN|_ version|version|NN|_ 0.5.9-r16|0.5.9-r16|NN|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ bwa|bwa|NN|_ aln|aln|NN|_ -|-|:|_ q|q|NN|_ 20|20|CD|_
Differentially|differentially|RB|_ expressed|express|VBD|_ genes|gene|NNS|_ were|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ processing|process|VBG|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ with|with|IN|_ edgeR|edger|NN|_ R|r|NN|_ library|library|NN|_ version|version|NN|_ 2.6.9|2.6.9|CD|_ .|.|.|_ Normalized|normalize|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ were|be|VBD|_ averaged|average|VBN|_ between|between|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ .|.|.|_
Differentially|differentially|RB|_ expressed|express|VBD|_ -LRB-|-lrb-|-LRB-|_ DE|de|NN|_ -RRB-|-rrb-|-RRB-|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ stress|stress|NN|_ evolved|evolve|VBD|_ strains|strain|NNS|_ were|be|VBD|_ found|find|VBN|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ expression|expression|NN|_ levels|level|NNS|_ in|in|IN|_ the|the|DT|_ reference|reference|NN|_ G500|g500|NN|_ strain|strain|NN|_ using|use|VBG|_ the|the|DT|_ edgeR|edger|NN|_ R|r|NN|_ package|package|NN|_ .|.|.|_
Genes|gene|NNS|_ with|with|IN|_ BH|bh|NN|_ -LRB-|-lrb-|-LRB-|_ Benjamini|Benjamini|NNP|_ and|and|CC|_ Hochberg|Hochberg|NNP|_ -RRB-|-rrb-|-RRB-|_ adjusted|adjust|VBN|_ p-values|p-value|NNS|_ below|below|IN|_ 0.05|0.05|CD|_ threshold|threshold|NN|_ were|be|VBD|_ selected|select|VBN|_ as|as|IN|_ DE|de|NN|_ genes|gene|NNS|_ .|.|.|_
Genes|gene|NNS|_ from|from|IN|_ the|the|DT|_ amplified|amplify|VBN|_ regions|region|NNS|_ in|in|IN|_ O500|o500|NN|_ -LRB-|-lrb-|-LRB-|_ 12-fold|12-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ P500|p500|NN|_ -LRB-|-lrb-|-LRB-|_ two-fold|two-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ strains|strain|NNS|_ are|be|VBP|_ significantly|significantly|RB|_ over-expressed|over-expressed|JJ|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ :|:|:|_ average|average|JJ|_ log|log|NN|_ Fold|Fold|NNP|_ Change|Change|NNP|_ for|for|IN|_ concentrations|concentration|NNS|_ is|be|VBZ|_ +3.6|+3.6|CD|_ and|and|CC|_ +0.8|+0.8|CD|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ with|with|IN|_ p-values|p-values|NN|_ <|<|JJR|_ 10-20|10-20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ file|file|NN|_ ;|;|:|_ includes|include|VBZ|_ :|:|:|_ gene|gene|NN|_ differential|differential|JJ|_ expression|expression|NN|_ levels|level|NNS|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ G500|g500|NN|_ strain|strain|NN|_ with|with|IN|_ corresponding|corresponding|JJ|_ p-values|p-value|NNS|_ and|and|CC|_ processed|process|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ normolized|normolized|NN|_ and|and|CC|_ averaged|average|VBD|_ between|between|IN|_ 2|2|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Linked|link|VBN|_ as|as|IN|_ supplementary|supplementary|JJ|_ file|file|NN|_ on|on|IN|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ 1st|1st|JJ|_ and|and|CC|_ 2nd|2nd|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ linker|linker|NN|_ ligation|ligation|NN|_ and|and|CC|_ size|size|NN|_ selection|selection|NN|_ subjected|subject|VBN|_ to|to|TO|_ shotgun|shotgun|NN|_ sequencing|sequencing|NN|_ using|use|VBG|_ single|single|JJ|_ read|read|NN|_ 40bp|40bp|JJ|_ read|read|NN|_ length|length|NN|_ runs|run|VBZ|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ GAII|GAII|NNP|_ .|.|.|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG|mg|NN|_ 1655|1655|CD|_
stress|stress|NN|_ :|:|:|_ osmotic|osmotic|JJ|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
technical|technical|JJ|_ replicates|replicate|VBZ|_ :|:|:|_ 2|2|CD|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
Vadim|Vadim|NNP|_ ,|,|,|_ ,|,|,|_ Mozhayskiy|Mozhayskiy|NNP|_
Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ reads|read|VBZ|_ were|be|VBD|_ filtered|filter|VBN|_ by|by|IN|_ SGA|SGA|NNP|_ version|version|NN|_ 0.9.9|0.9.9|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ sga|sga|NN|_ preprocess|preprocess|NN|_ -|-|:|_ q|q|NN|_ 10|10|CD|_ -|-|:|_ f|f|LS|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ 25|25|CD|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ trim|trim|JJ|_ 10|10|CD|_ ,|,|,|_ quality|quality|NN|_ filter|filter|NN|_ 10|10|CD|_ ,|,|,|_ minimal|minimal|JJ|_ length|length|NN|_ 25|25|CD|_ -RRB-|-rrb-|-RRB-|_
preprocessed|preprocessed|JJ|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ BWA|BWA|NNP|_ toolkit|toolkit|NN|_ version|version|NN|_ 0.5.9-r16|0.5.9-r16|NN|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ bwa|bwa|NN|_ aln|aln|NN|_ -|-|:|_ q|q|NN|_ 20|20|CD|_
Differentially|differentially|RB|_ expressed|express|VBD|_ genes|gene|NNS|_ were|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ processing|process|VBG|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ with|with|IN|_ edgeR|edger|NN|_ R|r|NN|_ library|library|NN|_ version|version|NN|_ 2.6.9|2.6.9|CD|_ .|.|.|_ Normalized|normalize|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ were|be|VBD|_ averaged|average|VBN|_ between|between|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ .|.|.|_
Differentially|differentially|RB|_ expressed|express|VBD|_ -LRB-|-lrb-|-LRB-|_ DE|de|NN|_ -RRB-|-rrb-|-RRB-|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ stress|stress|NN|_ evolved|evolve|VBD|_ strains|strain|NNS|_ were|be|VBD|_ found|find|VBN|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ expression|expression|NN|_ levels|level|NNS|_ in|in|IN|_ the|the|DT|_ reference|reference|NN|_ G500|g500|NN|_ strain|strain|NN|_ using|use|VBG|_ the|the|DT|_ edgeR|edger|NN|_ R|r|NN|_ package|package|NN|_ .|.|.|_
Genes|gene|NNS|_ with|with|IN|_ BH|bh|NN|_ -LRB-|-lrb-|-LRB-|_ Benjamini|Benjamini|NNP|_ and|and|CC|_ Hochberg|Hochberg|NNP|_ -RRB-|-rrb-|-RRB-|_ adjusted|adjust|VBN|_ p-values|p-value|NNS|_ below|below|IN|_ 0.05|0.05|CD|_ threshold|threshold|NN|_ were|be|VBD|_ selected|select|VBN|_ as|as|IN|_ DE|de|NN|_ genes|gene|NNS|_ .|.|.|_
Genes|gene|NNS|_ from|from|IN|_ the|the|DT|_ amplified|amplify|VBN|_ regions|region|NNS|_ in|in|IN|_ O500|o500|NN|_ -LRB-|-lrb-|-LRB-|_ 12-fold|12-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ P500|p500|NN|_ -LRB-|-lrb-|-LRB-|_ two-fold|two-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ strains|strain|NNS|_ are|be|VBP|_ significantly|significantly|RB|_ over-expressed|over-expressed|JJ|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ :|:|:|_ average|average|JJ|_ log|log|NN|_ Fold|Fold|NNP|_ Change|Change|NNP|_ for|for|IN|_ concentrations|concentration|NNS|_ is|be|VBZ|_ +3.6|+3.6|CD|_ and|and|CC|_ +0.8|+0.8|CD|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ with|with|IN|_ p-values|p-values|NN|_ <|<|JJR|_ 10-20|10-20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ file|file|NN|_ ;|;|:|_ includes|include|VBZ|_ :|:|:|_ gene|gene|NN|_ differential|differential|JJ|_ expression|expression|NN|_ levels|level|NNS|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ G500|g500|NN|_ strain|strain|NN|_ with|with|IN|_ corresponding|corresponding|JJ|_ p-values|p-value|NNS|_ and|and|CC|_ processed|process|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ normolized|normolized|NN|_ and|and|CC|_ averaged|average|VBD|_ between|between|IN|_ 2|2|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Linked|link|VBN|_ as|as|IN|_ supplementary|supplementary|JJ|_ file|file|NN|_ on|on|IN|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ 1st|1st|JJ|_ and|and|CC|_ 2nd|2nd|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ linker|linker|NN|_ ligation|ligation|NN|_ and|and|CC|_ size|size|NN|_ selection|selection|NN|_ subjected|subject|VBN|_ to|to|TO|_ shotgun|shotgun|NN|_ sequencing|sequencing|NN|_ using|use|VBG|_ single|single|JJ|_ read|read|NN|_ 40bp|40bp|JJ|_ read|read|NN|_ length|length|NN|_ runs|run|VBZ|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ GAII|GAII|NNP|_ .|.|.|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG|mg|NN|_ 1655|1655|CD|_
stress|stress|NN|_ :|:|:|_ acidic|acidic|JJ|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
technical|technical|JJ|_ replicates|replicate|VBZ|_ :|:|:|_ 2|2|CD|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ approx.|approx.|RB|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterial|bacterial|JJ|_ cell|cell|NN|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol/ethanol|phenol/ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ Phenol|phenol|NN|_ in|in|IN|_ EtOHabs|etohab|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_
Vadim|Vadim|NNP|_ ,|,|,|_ ,|,|,|_ Mozhayskiy|Mozhayskiy|NNP|_
The|The|NNP|_ original|original|JJ|_ image|image|NN|_ data|datum|NNS|_ is|be|VBZ|_ transfered|transfer|VBN|_ into|into|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ by|by|IN|_ base|base|NN|_ calling|call|VBG|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ DH10B|dh10b|NN|_ gene|gene|NN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ GI|GI|NNP|_ :|:|:|_ 170079663/NC|170079663/nc|NN|_ _|_|CD|_ 010473|010473|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
mRNA|mrna|NN|_ of|of|IN|_ prokaryotes|prokaryote|NNS|_ is|be|VBZ|_ enriched|enriched|JJ|_ just|just|RB|_ by|by|IN|_ removing|remove|VBG|_ rRNAs|rrna|NNS|_ from|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ Adding|add|VBG|_ the|the|DT|_ fragmentation|fragmentation|NN|_ buffer|buffer|NN|_ ,|,|,|_ the|the|DT|_ mRNA|mrna|NN|_ is|be|VBZ|_ interrupted|interrupted|JJ|_ to|to|TO|_ short|short|JJ|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ about|about|RB|_ 200|200|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ is|be|VBZ|_ synthesized|synthesize|VBN|_ by|by|IN|_ random|random|JJ|_ hexamer-primer|hexamer-primer|NN|_ using|use|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ as|as|IN|_ templates|template|NNS|_ .|.|.|_ Buffer|buffer|NN|_ ,|,|,|_ dNTPs|dntps|NN|_ ,|,|,|_ RNase|rnase|NN|_ H|h|NN|_ and|and|CC|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ I|I|PRP|_ are|be|VBP|_ added|add|VBN|_ to|to|TO|_ sythsize|sythsize|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ double|double|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ is|be|VBZ|_ purified|purify|VBN|_ with|with|IN|_ QiaQuick|QiaQuick|NNP|_ PCR|pcr|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ EB|EB|NNP|_ buffer|buffer|NN|_ for|for|IN|_ end|end|NN|_ repair|repair|NN|_ and|and|CC|_ single|single|JJ|_ nucleotide|nucleotide|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ adenine|adenine|NN|_ -RRB-|-rrb-|-RRB-|_ addition|addition|NN|_ .|.|.|_
sequencing|sequencing|NN|_ adaptors|adaptor|NNS|_ are|be|VBP|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ fragments|fragment|NNS|_ .|.|.|_ The|the|DT|_ required|require|VBN|_ fragments|fragment|NNS|_ is|be|VBZ|_ purified|purify|VBN|_ by|by|IN|_ agrose|agrose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ and|and|CC|_ enriched|enrich|VBN|_ by|by|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ .|.|.|_ The|the|DT|_ library|library|NN|_ products|product|NNS|_ are|be|VBP|_ ready|ready|JJ|_ for|for|IN|_ sequencing|sequencing|NN|_ analysis|analysis|NN|_ via|via|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ ™|™|SYM|_ 2000|2000|CD|_ .|.|.|_
37C|37c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ invitrogen|invitrogen|NN|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacture|manufacture|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instruction|instruction|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ extracts|extract|NNS|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ ,|,|,|_ Beverly|Beverly|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ quality|quality|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ also|also|RB|_ checked|check|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ rRNAs|rrna|NNS|_ was|be|VBD|_ subsquently|subsquently|RB|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ total|total|NN|_ mRNA|mrna|NN|_ following|follow|VBG|_ the|the|DT|_ instruction|instruction|NN|_ of|of|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNATM|rRNATM|NNP|_ Removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ no|no|DT|_ LL37|ll37|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
37C|37c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ invitrogen|invitrogen|NN|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacture|manufacture|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instruction|instruction|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ extracts|extract|NNS|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ ,|,|,|_ Beverly|Beverly|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ quality|quality|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ also|also|RB|_ checked|check|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ rRNAs|rrna|NNS|_ was|be|VBD|_ subsquently|subsquently|RB|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ total|total|NN|_ mRNA|mrna|NN|_ following|follow|VBG|_ the|the|DT|_ instruction|instruction|NN|_ of|of|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNATM|rRNATM|NNP|_ Removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WEI|WEI|NNP|_ ,|,|,|_ ,|,|,|_ LIU|LIU|NNP|_
The|The|NNP|_ original|original|JJ|_ image|image|NN|_ data|datum|NNS|_ is|be|VBZ|_ transfered|transfer|VBN|_ into|into|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ by|by|IN|_ base|base|NN|_ calling|call|VBG|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ DH10B|dh10b|NN|_ gene|gene|NN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ GI|GI|NNP|_ :|:|:|_ 170079663/NC|170079663/nc|NN|_ _|_|CD|_ 010473|010473|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
mRNA|mrna|NN|_ of|of|IN|_ prokaryotes|prokaryote|NNS|_ is|be|VBZ|_ enriched|enriched|JJ|_ just|just|RB|_ by|by|IN|_ removing|remove|VBG|_ rRNAs|rrna|NNS|_ from|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ Adding|add|VBG|_ the|the|DT|_ fragmentation|fragmentation|NN|_ buffer|buffer|NN|_ ,|,|,|_ the|the|DT|_ mRNA|mrna|NN|_ is|be|VBZ|_ interrupted|interrupted|JJ|_ to|to|TO|_ short|short|JJ|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ about|about|RB|_ 200|200|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ is|be|VBZ|_ synthesized|synthesize|VBN|_ by|by|IN|_ random|random|JJ|_ hexamer-primer|hexamer-primer|NN|_ using|use|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ as|as|IN|_ templates|template|NNS|_ .|.|.|_ Buffer|buffer|NN|_ ,|,|,|_ dNTPs|dntps|NN|_ ,|,|,|_ RNase|rnase|NN|_ H|h|NN|_ and|and|CC|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ I|I|PRP|_ are|be|VBP|_ added|add|VBN|_ to|to|TO|_ sythsize|sythsize|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ double|double|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ is|be|VBZ|_ purified|purify|VBN|_ with|with|IN|_ QiaQuick|QiaQuick|NNP|_ PCR|pcr|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ EB|EB|NNP|_ buffer|buffer|NN|_ for|for|IN|_ end|end|NN|_ repair|repair|NN|_ and|and|CC|_ single|single|JJ|_ nucleotide|nucleotide|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ adenine|adenine|NN|_ -RRB-|-rrb-|-RRB-|_ addition|addition|NN|_ .|.|.|_
sequencing|sequencing|NN|_ adaptors|adaptor|NNS|_ are|be|VBP|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ fragments|fragment|NNS|_ .|.|.|_ The|the|DT|_ required|require|VBN|_ fragments|fragment|NNS|_ is|be|VBZ|_ purified|purify|VBN|_ by|by|IN|_ agrose|agrose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ and|and|CC|_ enriched|enrich|VBN|_ by|by|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ .|.|.|_ The|the|DT|_ library|library|NN|_ products|product|NNS|_ are|be|VBP|_ ready|ready|JJ|_ for|for|IN|_ sequencing|sequencing|NN|_ analysis|analysis|NN|_ via|via|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ ™|™|SYM|_ 2000|2000|CD|_ .|.|.|_
37C|37c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ invitrogen|invitrogen|NN|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacture|manufacture|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instruction|instruction|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ extracts|extract|NNS|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ ,|,|,|_ Beverly|Beverly|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ quality|quality|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ also|also|RB|_ checked|check|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ rRNAs|rrna|NNS|_ was|be|VBD|_ subsquently|subsquently|RB|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ total|total|NN|_ mRNA|mrna|NN|_ following|follow|VBG|_ the|the|DT|_ instruction|instruction|NN|_ of|of|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNATM|rRNATM|NNP|_ Removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ LL37|ll37|NN|_ expression|expression|NN|_ induced|induce|VBD|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
37C|37c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ invitrogen|invitrogen|NN|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacture|manufacture|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instruction|instruction|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ extracts|extract|NNS|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ ,|,|,|_ Beverly|Beverly|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ quality|quality|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ also|also|RB|_ checked|check|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ rRNAs|rrna|NNS|_ was|be|VBD|_ subsquently|subsquently|RB|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ total|total|NN|_ mRNA|mrna|NN|_ following|follow|VBG|_ the|the|DT|_ instruction|instruction|NN|_ of|of|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNATM|rRNATM|NNP|_ Removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WEI|WEI|NNP|_ ,|,|,|_ ,|,|,|_ LIU|LIU|NNP|_
The|The|NNP|_ original|original|JJ|_ image|image|NN|_ data|datum|NNS|_ is|be|VBZ|_ transfered|transfer|VBN|_ into|into|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ by|by|IN|_ base|base|NN|_ calling|call|VBG|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ DH10B|dh10b|NN|_ gene|gene|NN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ GI|GI|NNP|_ :|:|:|_ 170079663/NC|170079663/nc|NN|_ _|_|CD|_ 010473|010473|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
mRNA|mrna|NN|_ of|of|IN|_ prokaryotes|prokaryote|NNS|_ is|be|VBZ|_ enriched|enriched|JJ|_ just|just|RB|_ by|by|IN|_ removing|remove|VBG|_ rRNAs|rrna|NNS|_ from|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ Adding|add|VBG|_ the|the|DT|_ fragmentation|fragmentation|NN|_ buffer|buffer|NN|_ ,|,|,|_ the|the|DT|_ mRNA|mrna|NN|_ is|be|VBZ|_ interrupted|interrupted|JJ|_ to|to|TO|_ short|short|JJ|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ about|about|RB|_ 200|200|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ is|be|VBZ|_ synthesized|synthesize|VBN|_ by|by|IN|_ random|random|JJ|_ hexamer-primer|hexamer-primer|NN|_ using|use|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ as|as|IN|_ templates|template|NNS|_ .|.|.|_ Buffer|buffer|NN|_ ,|,|,|_ dNTPs|dntps|NN|_ ,|,|,|_ RNase|rnase|NN|_ H|h|NN|_ and|and|CC|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ I|I|PRP|_ are|be|VBP|_ added|add|VBN|_ to|to|TO|_ sythsize|sythsize|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ double|double|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ is|be|VBZ|_ purified|purify|VBN|_ with|with|IN|_ QiaQuick|QiaQuick|NNP|_ PCR|pcr|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ EB|EB|NNP|_ buffer|buffer|NN|_ for|for|IN|_ end|end|NN|_ repair|repair|NN|_ and|and|CC|_ single|single|JJ|_ nucleotide|nucleotide|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ adenine|adenine|NN|_ -RRB-|-rrb-|-RRB-|_ addition|addition|NN|_ .|.|.|_
sequencing|sequencing|NN|_ adaptors|adaptor|NNS|_ are|be|VBP|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ fragments|fragment|NNS|_ .|.|.|_ The|the|DT|_ required|require|VBN|_ fragments|fragment|NNS|_ is|be|VBZ|_ purified|purify|VBN|_ by|by|IN|_ agrose|agrose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ and|and|CC|_ enriched|enrich|VBN|_ by|by|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ .|.|.|_ The|the|DT|_ library|library|NN|_ products|product|NNS|_ are|be|VBP|_ ready|ready|JJ|_ for|for|IN|_ sequencing|sequencing|NN|_ analysis|analysis|NN|_ via|via|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ ™|™|SYM|_ 2000|2000|CD|_ .|.|.|_
37C|37c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ invitrogen|invitrogen|NN|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacture|manufacture|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instruction|instruction|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ extracts|extract|NNS|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ ,|,|,|_ Beverly|Beverly|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ quality|quality|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ also|also|RB|_ checked|check|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ rRNAs|rrna|NNS|_ was|be|VBD|_ subsquently|subsquently|RB|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ total|total|NN|_ mRNA|mrna|NN|_ following|follow|VBG|_ the|the|DT|_ instruction|instruction|NN|_ of|of|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNATM|rRNATM|NNP|_ Removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ no|no|DT|_ LL37|ll37|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ anaerobic|anaerobic|JJ|_
37C|37c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ invitrogen|invitrogen|NN|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacture|manufacture|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instruction|instruction|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ extracts|extract|NNS|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ ,|,|,|_ Beverly|Beverly|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ quality|quality|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ also|also|RB|_ checked|check|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ rRNAs|rrna|NNS|_ was|be|VBD|_ subsquently|subsquently|RB|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ total|total|NN|_ mRNA|mrna|NN|_ following|follow|VBG|_ the|the|DT|_ instruction|instruction|NN|_ of|of|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNATM|rRNATM|NNP|_ Removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WEI|WEI|NNP|_ ,|,|,|_ ,|,|,|_ LIU|LIU|NNP|_
The|The|NNP|_ original|original|JJ|_ image|image|NN|_ data|datum|NNS|_ is|be|VBZ|_ transfered|transfer|VBN|_ into|into|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ by|by|IN|_ base|base|NN|_ calling|call|VBG|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ DH10B|dh10b|NN|_ gene|gene|NN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ GI|GI|NNP|_ :|:|:|_ 170079663/NC|170079663/nc|NN|_ _|_|CD|_ 010473|010473|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
mRNA|mrna|NN|_ of|of|IN|_ prokaryotes|prokaryote|NNS|_ is|be|VBZ|_ enriched|enriched|JJ|_ just|just|RB|_ by|by|IN|_ removing|remove|VBG|_ rRNAs|rrna|NNS|_ from|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ Adding|add|VBG|_ the|the|DT|_ fragmentation|fragmentation|NN|_ buffer|buffer|NN|_ ,|,|,|_ the|the|DT|_ mRNA|mrna|NN|_ is|be|VBZ|_ interrupted|interrupted|JJ|_ to|to|TO|_ short|short|JJ|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ about|about|RB|_ 200|200|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ is|be|VBZ|_ synthesized|synthesize|VBN|_ by|by|IN|_ random|random|JJ|_ hexamer-primer|hexamer-primer|NN|_ using|use|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ as|as|IN|_ templates|template|NNS|_ .|.|.|_ Buffer|buffer|NN|_ ,|,|,|_ dNTPs|dntps|NN|_ ,|,|,|_ RNase|rnase|NN|_ H|h|NN|_ and|and|CC|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ I|I|PRP|_ are|be|VBP|_ added|add|VBN|_ to|to|TO|_ sythsize|sythsize|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ double|double|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ is|be|VBZ|_ purified|purify|VBN|_ with|with|IN|_ QiaQuick|QiaQuick|NNP|_ PCR|pcr|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ EB|EB|NNP|_ buffer|buffer|NN|_ for|for|IN|_ end|end|NN|_ repair|repair|NN|_ and|and|CC|_ single|single|JJ|_ nucleotide|nucleotide|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ adenine|adenine|NN|_ -RRB-|-rrb-|-RRB-|_ addition|addition|NN|_ .|.|.|_
sequencing|sequencing|NN|_ adaptors|adaptor|NNS|_ are|be|VBP|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ fragments|fragment|NNS|_ .|.|.|_ The|the|DT|_ required|require|VBN|_ fragments|fragment|NNS|_ is|be|VBZ|_ purified|purify|VBN|_ by|by|IN|_ agrose|agrose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ and|and|CC|_ enriched|enrich|VBN|_ by|by|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ .|.|.|_ The|the|DT|_ library|library|NN|_ products|product|NNS|_ are|be|VBP|_ ready|ready|JJ|_ for|for|IN|_ sequencing|sequencing|NN|_ analysis|analysis|NN|_ via|via|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ ™|™|SYM|_ 2000|2000|CD|_ .|.|.|_
37C|37c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ invitrogen|invitrogen|NN|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacture|manufacture|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instruction|instruction|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ extracts|extract|NNS|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ ,|,|,|_ Beverly|Beverly|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ quality|quality|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ also|also|RB|_ checked|check|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ rRNAs|rrna|NNS|_ was|be|VBD|_ subsquently|subsquently|RB|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ total|total|NN|_ mRNA|mrna|NN|_ following|follow|VBG|_ the|the|DT|_ instruction|instruction|NN|_ of|of|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNATM|rRNATM|NNP|_ Removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ LL37|ll37|NN|_ expression|expression|NN|_ induced|induce|VBD|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ anaerobic|anaerobic|JJ|_
37C|37c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.coli|e.coli|NNS|_ Top|top|JJ|_ 10|10|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ invitrogen|invitrogen|NN|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacture|manufacture|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ instruction|instruction|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ extracts|extract|NNS|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ ,|,|,|_ Beverly|Beverly|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ quality|quality|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ also|also|RB|_ checked|check|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ rRNAs|rrna|NNS|_ was|be|VBD|_ subsquently|subsquently|RB|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ total|total|NN|_ mRNA|mrna|NN|_ following|follow|VBG|_ the|the|DT|_ instruction|instruction|NN|_ of|of|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNATM|rRNATM|NNP|_ Removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WEI|WEI|NNP|_ ,|,|,|_ ,|,|,|_ LIU|LIU|NNP|_
Xpression|xpression|NN|_ -LRB-|-lrb-|-LRB-|_ https://depts.washington.edu/cshlab/html/rnaseq.html|https://depts.washington.edu/cshlab/html/rnaseq.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ processing|processing|NN|_ .|.|.|_
Xpression|xpression|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ and|and|CC|_ trimming|trim|VBG|_ reads|read|VBZ|_ .|.|.|_
Reference|Reference|NNP|_ files|file|VBZ|_ for|for|IN|_ the|the|DT|_ genome|genome|NN|_ sequence|sequence|NN|_ being|be|VBG|_ queried|query|VBN|_ ,|,|,|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 012971|012971|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ uploaded|upload|VBN|_ .|.|.|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ FASTQ|fastq|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ processed|process|VBN|_ by|by|IN|_ Xpression|xpression|NN|_ and|and|CC|_ only|only|RB|_ the|the|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ recorded|record|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ based|base|VBN|_ on|on|IN|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ uniquely|uniquely|RB|_ mapped|map|VBD|_ reads|read|VBZ|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ gi|gi|NN|_ ||||SYM|_ 387825439|387825439|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ from|from|IN|_ C.|C.|NNP|_ glutamicum|glutamicum|NN|_ cells|cell|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_ ®|®|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ NucleoSpin|NucleoSpin|NNP|_ ®|®|NNP|_ -LRB-|-lrb-|-LRB-|_ Macherey-Nagel|Macherey-Nagel|NNP|_ ,|,|,|_ Düren|Düren|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ resuspended|resuspend|VBN|_ in|in|IN|_ TRIzol|trizol|NN|_ ®|®|NN|_ reagent|reagent|NN|_ ,|,|,|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ vial|vial|NN|_ containing|contain|VBG|_ Lysing|lyse|VBG|_ Matrix|Matrix|NNP|_ B|B|NNP|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedicals|biomedical|NNS|_ ,|,|,|_ Solon|Solon|NNP|_ ,|,|,|_ OH|oh|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ lysis|lysis|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ a|a|DT|_ NucleoSpin|NucleoSpin|NNP|_ ®|®|NN|_ RNA|rna|NN|_ II|ii|CD|_ kit|kit|NN|_ for|for|IN|_ purification|purification|NN|_ .|.|.|_
First|First|NNP|_ and|and|CC|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ Ovation|Ovation|NNP|_ ®|®|NNP|_ Prokaryotic|Prokaryotic|NNP|_ RNA-Seq|RNA-Seq|NNP|_ System|System|NNP|_ -LRB-|-lrb-|-LRB-|_ NuGEN|NuGEN|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Carlos|Carlos|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ NuGEN|nugen|NN|_ 's|'s|POS|_ Encore|encore|NN|_ NGS|ngs|NN|_ Library|Library|NNP|_ System|System|NNP|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ construct|construct|VB|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ the|the|DT|_ IlluminaHiSeq|IlluminaHiSeq|NNP|_ platform|platform|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ fermenter|fermenter|NN|_ containing|contain|VBG|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED supplemented|supplement|VBN|_ with|with|IN|_ 3|3|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ antibiotics|antibiotic|NNS|_ .|.|.|_ The|the|DT|_ fermentors|fermentor|NNS|_ were|be|VBD|_ operated|operate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ with|with|IN|_ aeration|aeration|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ mL/min|ml/min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Flow|flow|NN|_ rate|rate|NN|_ was|be|VBD|_ 1.162|1.162|CD|_ ml/min|ml/min|NN|_ -LRB-|-lrb-|-LRB-|_ dilution|dilution|NN|_ rate|rate|NN|_ 0,7|0,7|CD|_ /|/|:|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ pellets|pellet|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA|rna|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ wild-type|wild-type|JJ|_
condition|condition|NN|_ :|:|:|_ LB|lb|NN|_ +3|+3|CD|_ g/L|g/L|NNP|_ Glc|Glc|NNP|_ +0.1|+0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ fermenter|fermenter|NN|_ containing|contain|VBG|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED supplemented|supplement|VBN|_ with|with|IN|_ 3|3|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ antibiotics|antibiotic|NNS|_ .|.|.|_ The|the|DT|_ fermentors|fermentor|NNS|_ were|be|VBD|_ operated|operate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ with|with|IN|_ aeration|aeration|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ mL/min|ml/min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Flow|flow|NN|_ rate|rate|NN|_ was|be|VBD|_ 1.162|1.162|CD|_ ml/min|ml/min|NN|_ -LRB-|-lrb-|-LRB-|_ dilution|dilution|NN|_ rate|rate|NN|_ 0,7|0,7|CD|_ /|/|:|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ pellets|pellet|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA|rna|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Hyojung|hyojung|NN|_ ,|,|,|_ ,|,|,|_ Lee|Lee|NNP|_
Xpression|xpression|NN|_ -LRB-|-lrb-|-LRB-|_ https://depts.washington.edu/cshlab/html/rnaseq.html|https://depts.washington.edu/cshlab/html/rnaseq.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ processing|processing|NN|_ .|.|.|_
Xpression|xpression|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ and|and|CC|_ trimming|trim|VBG|_ reads|read|VBZ|_ .|.|.|_
Reference|Reference|NNP|_ files|file|VBZ|_ for|for|IN|_ the|the|DT|_ genome|genome|NN|_ sequence|sequence|NN|_ being|be|VBG|_ queried|query|VBN|_ ,|,|,|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 012971|012971|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ uploaded|upload|VBN|_ .|.|.|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ FASTQ|fastq|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ processed|process|VBN|_ by|by|IN|_ Xpression|xpression|NN|_ and|and|CC|_ only|only|RB|_ the|the|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ recorded|record|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ based|base|VBN|_ on|on|IN|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ uniquely|uniquely|RB|_ mapped|map|VBD|_ reads|read|VBZ|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ gi|gi|NN|_ ||||SYM|_ 387825439|387825439|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ from|from|IN|_ C.|C.|NNP|_ glutamicum|glutamicum|NN|_ cells|cell|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_ ®|®|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ NucleoSpin|NucleoSpin|NNP|_ ®|®|NNP|_ -LRB-|-lrb-|-LRB-|_ Macherey-Nagel|Macherey-Nagel|NNP|_ ,|,|,|_ Düren|Düren|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ resuspended|resuspend|VBN|_ in|in|IN|_ TRIzol|trizol|NN|_ ®|®|NN|_ reagent|reagent|NN|_ ,|,|,|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ vial|vial|NN|_ containing|contain|VBG|_ Lysing|lyse|VBG|_ Matrix|Matrix|NNP|_ B|B|NNP|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedicals|biomedical|NNS|_ ,|,|,|_ Solon|Solon|NNP|_ ,|,|,|_ OH|oh|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ lysis|lysis|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ a|a|DT|_ NucleoSpin|NucleoSpin|NNP|_ ®|®|NN|_ RNA|rna|NN|_ II|ii|CD|_ kit|kit|NN|_ for|for|IN|_ purification|purification|NN|_ .|.|.|_
First|First|NNP|_ and|and|CC|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ Ovation|Ovation|NNP|_ ®|®|NNP|_ Prokaryotic|Prokaryotic|NNP|_ RNA-Seq|RNA-Seq|NNP|_ System|System|NNP|_ -LRB-|-lrb-|-LRB-|_ NuGEN|NuGEN|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Carlos|Carlos|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ NuGEN|nugen|NN|_ 's|'s|POS|_ Encore|encore|NN|_ NGS|ngs|NN|_ Library|Library|NNP|_ System|System|NNP|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ construct|construct|VB|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ the|the|DT|_ IlluminaHiSeq|IlluminaHiSeq|NNP|_ platform|platform|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ fermenter|fermenter|NN|_ containing|contain|VBG|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED supplemented|supplement|VBN|_ with|with|IN|_ 3|3|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ antibiotics|antibiotic|NNS|_ .|.|.|_ The|the|DT|_ fermentors|fermentor|NNS|_ were|be|VBD|_ operated|operate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ with|with|IN|_ aeration|aeration|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ mL/min|ml/min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Flow|flow|NN|_ rate|rate|NN|_ was|be|VBD|_ 1.162|1.162|CD|_ ml/min|ml/min|NN|_ -LRB-|-lrb-|-LRB-|_ dilution|dilution|NN|_ rate|rate|NN|_ 0,7|0,7|CD|_ /|/|:|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ pellets|pellet|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA|rna|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ Pck|pck|NN|_ over-expressed|over-expressed|JJ|_
condition|condition|NN|_ :|:|:|_ LB|lb|NN|_ +3|+3|CD|_ g/L|g/L|NNP|_ Glc|Glc|NNP|_ +0.1|+0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ +|+|CC|_ 50μg/ml|50μg/ml|JJ|_ Amp|amp|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ fermenter|fermenter|NN|_ containing|contain|VBG|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED supplemented|supplement|VBN|_ with|with|IN|_ 3|3|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ antibiotics|antibiotic|NNS|_ .|.|.|_ The|the|DT|_ fermentors|fermentor|NNS|_ were|be|VBD|_ operated|operate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ with|with|IN|_ aeration|aeration|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ mL/min|ml/min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Flow|flow|NN|_ rate|rate|NN|_ was|be|VBD|_ 1.162|1.162|CD|_ ml/min|ml/min|NN|_ -LRB-|-lrb-|-LRB-|_ dilution|dilution|NN|_ rate|rate|NN|_ 0,7|0,7|CD|_ /|/|:|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ pellets|pellet|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA|rna|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Hyojung|hyojung|NN|_ ,|,|,|_ ,|,|,|_ Lee|Lee|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_
genotype|genotype|NN|_ :|:|:|_ pHDB3|phdb3|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_
genotype|genotype|NN|_ :|:|:|_ pLCV1|plcv1|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ 0.5|0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ 0.5|0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ 0.5|0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ 0.5|0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ SgrR|sgrr|NN|TF
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ 0.5|0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ SgrR|sgrr|NN|TF
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ 0.5|0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ SgrR|sgrr|NN|TF
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ sgrS|sgrs|NN|GEN
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ sgrS|sgrs|NN|GEN
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ sgrS|sgrs|NN|GEN
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ sgrS|sgrs|NN|GEN
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ sgrS|sgrs|NN|GEN
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ sgrS|sgrs|NN|GEN
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ 0.5|0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ 0.5|0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ 0.5|0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ CV108|cv108|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ CV108|cv108|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ CV108|cv108|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ CV108|cv108|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ CV108|cv108|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ CV108|cv108|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ 2-DG|2-dg|JJ|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ 2-DG|2-dg|JJ|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
RNA-Seq|rna-seq|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ 2-DG|2-dg|JJ|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
Brian|Brian|NNP|_ ,|,|,|_ ,|,|,|_ Tjaden|Tjaden|NNP|_
The|The|NNP|_ sample|sample|NN|_ sources|source|NNS|_ of|of|IN|_ individual|individual|JJ|_ reads|read|VBZ|_ were|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ the|the|DT|_ barcoding|barcoding|NN|_ .|.|.|_ The|the|DT|_ barcodes|barcode|NNS|_ for|for|IN|_ the|the|DT|_ minus|minus|NN|_ and|and|CC|_ plus|plus|CC|_ TAP|tap|NN|_ treatments|treatment|NNS|_ were|be|VBD|_ ACTTGA|ACTTGA|NNP|_ and|and|CC|_ CGATGT|CGATGT|NNP|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ for|for|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ RNA|rna|NN|_ ,|,|,|_ and|and|CC|_ CAGATC|CAGATC|NNP|_ and|and|CC|_ ATCACG|ATCACG|NNP|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ for|for|IN|_ the|the|DT|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ RNA|rna|NN|_ .|.|.|_
RNA|rna|NN|_ sequences|sequence|NNS|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ two|two|CD|_ differential|differential|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ processed|process|VBN|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ corresponding|corresponding|JJ|_ genomes|genome|NNS|_ as|as|IN|_ a|a|DT|_ service|service|NN|_ provided|provide|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -LRB-|-lrb-|-LRB-|_ www.vertis-biotech.com|www.vertis-biotech.com|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ This|this|DT|_ involved|involved|JJ|_ trimming|trim|VBG|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ masking|mask|VBG|_ for|for|IN|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ .|.|.|_
For|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4|4|CD|_ libraries|library|NNS|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ bacterial|bacterial|JJ|_ samples|sample|NNS|_ x|x|CC|_ 2|2|CD|_ treatments|treatment|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ we|we|PRP|_ counted|count|VBD|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ times|time|NNS|_ each|each|DT|_ nucleotide|nucleotide|NN|_ position|position|NN|_ was|be|VBD|_ the|the|DT|_ first|first|JJ|_ in|in|IN|_ a|a|DT|_ sequence|sequence|NN|_ read|read|VBN|_ using|use|VBG|_ a|a|DT|_ simple|simple|JJ|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ unpubl|unpubl|NN|_ .|.|.|_ resource|resource|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ were|be|VBD|_ then|then|RB|_ processed|process|VBN|_ separately|separately|RB|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ The|the|DT|_ reference|reference|NN|_ genomes|genome|NNS|_ used|use|VBN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ strain|strain|NN|_ BW25113|bw25113|NN|_ and|and|CC|_ S.|S.|NNP|_ coelicolor|coelicolor|VBP|_ A3|a3|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ M145|m145|NN|_ were|be|VBD|_ U00096|u00096|NN|_ .2|.2|NN|_ and|and|CC|_ AL645882|al645882|NN|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BedGraphs|bedgraph|NNS|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ TAP|tap|NN|_ treatment|treatment|NN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ Separate|separate|JJ|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ pellet|pellet|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ using|use|VBG|_ a|a|DT|_ well-established|well-established|JJ|_ ,|,|,|_ published|publish|VBN|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ .|.|.|_ In|in|IN|_ RNA|rna|NN|_ Turnover|turnover|NN|_ in|in|IN|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Archaea|Archaea|NNP|_ and|and|CC|_ Organelles|Organelles|NNP|_ ,|,|,|_ Vol|Vol|NNP|_ 447|447|CD|_ -LRB-|-lrb-|-LRB-|_ ed|ed|VBN|_ .|.|.|_ LE|LE|NNP|_ Maquat|Maquat|NNP|_ ,|,|,|_ CM|cm|NN|_ Arraiano|arraiano|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pp.|pp.|NN|_ 215|215|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ of|of|IN|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ Kirby|Kirby|NNP|_ mix|mix|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ .|.|.|_ Practical|Practical|NNP|_ Streptomyces|Streptomyces|NNP|_ Genetics|Genetics|NNP|_ .|.|.|_ The|the|DT|_ John|John|NNP|_ Innes|Innes|NNP|_ Foundation|Foundation|NNP|_ ,|,|,|_ Norwich|Norwich|NNP|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ µL|µl|NN|_ per|per|IN|_ 1|1|CD|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ unit|unit|NN|_ ,|,|,|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ Lysing|lyse|VBG|_ Matrix|Matrix|NNP|_ B|B|NNP|_ tubes|tube|NNS|_ containing|contain|VBG|_ fine|fine|JJ|_ silica|silica|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ high-speed|high-speed|JJ|_ benchtop|benchtop|NN|_ homogenizer|homogenizer|NN|_ -LRB-|-lrb-|-LRB-|_ Fastprep-24|fastprep-24|NN|_ ,|,|,|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ;|;|:|_ set|set|VBN|_ at|at|IN|_ 6.5|6.5|CD|_ M/s|m/s|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ three|three|CD|_ cycles|cycle|NNS|_ of|of|IN|_ homogenisation|homogenisation|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ with|with|IN|_ cooling|cooling|NN|_ between|between|IN|_ each|each|DT|_ cycle|cycle|NN|_ in|in|IN|_ an|a|DT|_ ice-water|ice-water|JJ|_ bath|bath|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ lysates|lysate|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ acidic|acidic|JJ|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ :|:|:|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ :|:|:|_ 50|50|CD|_ :|:|:|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ chloroform|chloroform|NN|_ :|:|:|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -LRB-|-lrb-|-LRB-|_ 49|49|CD|_ :|:|:|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Nucleic|nucleic|JJ|_ acid|acid|NN|_ in|in|IN|_ the|the|DT|_ aqueous|aqueous|JJ|_ phase|phase|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ adding|add|VBG|_ NaCl|nacl|NN|_ to|to|TO|_ 150|150|CD|_ mM|mm|NN|KWSUPP and|and|CC|_ 2.5|2.5|CD|_ x|x|CC|_ volumes|volume|NNS|_ of|of|IN|_ 100|100|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ ethanol|ethanol|NN|_ ,|,|,|_ chilling|chill|VBG|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 13,000|13,000|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ nucleic|nucleic|JJ|_ acid|acid|NN|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ 700|700|CD|_ µL|µl|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ ethanol|ethanol|NN|_ ,|,|,|_ air|air|NN|_ dried|dry|VBD|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNase-free|rnase-free|JJ|_ water|water|NN|_ .|.|.|_ Contaminating|contaminate|VBG|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ both|both|DT|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ S.|s.|FW|_ coelicolor|coelicolor|FW|_ by|by|IN|_ incubating|incubate|VBG|_ with|with|IN|_ DNase|dnase|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ the|the|DT|_ vendor|vendor|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ a|a|DT|_ NanoDropTM|nanodroptm|NN|_ 1000|1000|CD|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ -LRB-|-lrb-|-LRB-|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ enriched|enrich|VBN|_ for|for|IN|_ mRNA|mrna|NN|_ using|use|VBG|_ MICROBExpress-Bacteria|microbexpress-bacteria|JJ|_ beads|bead|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -LRB-|-lrb-|-LRB-|_ www.vertis-biotech.com|www.vertis-biotech.com|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ a|a|DT|_ service|service|NN|_ that|that|WDT|_ included|include|VBD|_ treating|treat|VBG|_ an|a|DT|_ aliquot|aliquot|NN|_ of|of|IN|_ each|each|DT|_ RNA|rna|NN|_ sample|sample|NN|_ with|with|IN|_ TAP|tap|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ sequencing|sequencing|NN|_ adaptor|adaptor|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ transcripts|transcript|NNS|_ prior|prior|RB|_ to|to|TO|_ fragmentation|fragmentation|NN|_ ,|,|,|_ thereby|thereby|RB|_ allowing|allow|VBG|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ both|both|DT|_ long|long|JJ|_ and|and|CC|_ short|short|JJ|_ transcripts|transcript|NNS|_ to|to|TO|_ be|be|VB|_ detected|detect|VBN|_ .|.|.|_ Each|each|DT|_ of|of|IN|_ the|the|DT|_ 4|4|CD|_ libraries|library|NNS|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ a|a|DT|_ different|different|JJ|_ barcode|barcode|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ strain|strain|NN|_ BW25113|bw25113|NN|_ -LRB-|-lrb-|-LRB-|_ Datsenko|Datsenko|NNP|_ &|&|CC|_ Wanner|Wanner|NNP|_ 2000|2000|CD|_ .|.|.|_ PNAS|PNAS|NNP|_ 97|97|CD|_ :|:|:|_ 6640|6640|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ cultivated|cultivate|VBN|_ in|in|IN|_ 100|100|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ 1972|1972|CD|_ .|.|.|_ In|in|IN|_ :|:|:|_ Experiments|experiment|NNS|_ in|in|IN|_ molecular|molecular|JJ|_ genetics|genetics|NNS|_ .|.|.|_ Cold|Cold|NNP|_ Spring|Spring|NNP|_ Harbor|Harbor|NNP|_ Laboratory|Laboratory|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ mL|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ an|a|DT|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ 0.6|0.6|CD|_ .|.|.|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ A3|a3|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ M145|m145|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ .|.|.|_ Practical|Practical|NNP|_ Streptomyces|Streptomyces|NNP|_ Genetics|Genetics|NNP|_ .|.|.|_ The|the|DT|_ John|John|NNP|_ Innes|Innes|NNP|_ Foundation|Foundation|NNP|_ ,|,|,|_ Norwich|Norwich|NNP|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ YEME|yeme|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ the|the|DT|_ mycelia|mycelia|NN|_ became|become|VBD|_ pigmented|pigmented|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
E.|e.|FW|_ coli|coli|FW|_ batch|batch|NN|_ culture|culture|NN|_ without|without|IN|_ TAP|tap|NN|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ ,|,|,|_ a|a|DT|_ one-eighth|one-eighth|NN|_ volume|volume|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ ethanol|ethanol|NN|_ ;|;|:|_ 5|5|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ culture|culture|NN|_ to|to|TO|_ inhibit|inhibit|VB|_ cell|cell|NN|_ metabolism|metabolism|NN|_ -LRB-|-lrb-|-LRB-|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ .|.|.|_ In|in|IN|_ RNA|rna|NN|_ Turnover|turnover|NN|_ in|in|IN|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Archaea|Archaea|NNP|_ and|and|CC|_ Organelles|Organelles|NNP|_ ,|,|,|_ Vol|Vol|NNP|_ 447|447|CD|_ -LRB-|-lrb-|-LRB-|_ ed|ed|VBN|_ .|.|.|_ LE|LE|NNP|_ Maquat|Maquat|NNP|_ ,|,|,|_ CM|cm|NN|_ Arraiano|arraiano|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pp.|pp.|NN|_ 215|215|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ When|when|WRB|_ necessary|necessary|JJ|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype|genotype|NN|_ :|:|:|_ wild-type|wild-type|JJ|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ strain|strain|NN|_ BW25113|bw25113|NN|_ -LRB-|-lrb-|-LRB-|_ Datsenko|Datsenko|NNP|_ &|&|CC|_ Wanner|Wanner|NNP|_ 2000|2000|CD|_ .|.|.|_ PNAS|PNAS|NNP|_ 97|97|CD|_ :|:|:|_ 6640|6640|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ cultivated|cultivate|VBN|_ in|in|IN|_ 100|100|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ 1972|1972|CD|_ .|.|.|_ In|in|IN|_ :|:|:|_ Experiments|experiment|NNS|_ in|in|IN|_ molecular|molecular|JJ|_ genetics|genetics|NNS|_ .|.|.|_ Cold|Cold|NNP|_ Spring|Spring|NNP|_ Harbor|Harbor|NNP|_ Laboratory|Laboratory|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ mL|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ an|a|DT|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ 0.6|0.6|CD|_ .|.|.|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ A3|a3|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ M145|m145|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ .|.|.|_ Practical|Practical|NNP|_ Streptomyces|Streptomyces|NNP|_ Genetics|Genetics|NNP|_ .|.|.|_ The|the|DT|_ John|John|NNP|_ Innes|Innes|NNP|_ Foundation|Foundation|NNP|_ ,|,|,|_ Norwich|Norwich|NNP|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ YEME|yeme|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ the|the|DT|_ mycelia|mycelia|NN|_ became|become|VBD|_ pigmented|pigmented|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
E.|e.|FW|_ coli|coli|FW|_ batch|batch|NN|_ culture|culture|NN|_ without|without|IN|_ TAP|tap|NN|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ ,|,|,|_ a|a|DT|_ one-eighth|one-eighth|NN|_ volume|volume|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ ethanol|ethanol|NN|_ ;|;|:|_ 5|5|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ culture|culture|NN|_ to|to|TO|_ inhibit|inhibit|VB|_ cell|cell|NN|_ metabolism|metabolism|NN|_ -LRB-|-lrb-|-LRB-|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ .|.|.|_ In|in|IN|_ RNA|rna|NN|_ Turnover|turnover|NN|_ in|in|IN|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Archaea|Archaea|NNP|_ and|and|CC|_ Organelles|Organelles|NNP|_ ,|,|,|_ Vol|Vol|NNP|_ 447|447|CD|_ -LRB-|-lrb-|-LRB-|_ ed|ed|VBN|_ .|.|.|_ LE|LE|NNP|_ Maquat|Maquat|NNP|_ ,|,|,|_ CM|cm|NN|_ Arraiano|arraiano|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pp.|pp.|NN|_ 215|215|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ When|when|WRB|_ necessary|necessary|JJ|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_
David|David|NNP|_ ,|,|,|_ ,|,|,|_ Romero|Romero|NNP|_ A.|A.|NNP|_
The|The|NNP|_ sample|sample|NN|_ sources|source|NNS|_ of|of|IN|_ individual|individual|JJ|_ reads|read|VBZ|_ were|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ the|the|DT|_ barcoding|barcoding|NN|_ .|.|.|_ The|the|DT|_ barcodes|barcode|NNS|_ for|for|IN|_ the|the|DT|_ minus|minus|NN|_ and|and|CC|_ plus|plus|CC|_ TAP|tap|NN|_ treatments|treatment|NNS|_ were|be|VBD|_ ACTTGA|ACTTGA|NNP|_ and|and|CC|_ CGATGT|CGATGT|NNP|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ for|for|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ RNA|rna|NN|_ ,|,|,|_ and|and|CC|_ CAGATC|CAGATC|NNP|_ and|and|CC|_ ATCACG|ATCACG|NNP|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ for|for|IN|_ the|the|DT|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ RNA|rna|NN|_ .|.|.|_
RNA|rna|NN|_ sequences|sequence|NNS|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ two|two|CD|_ differential|differential|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ processed|process|VBN|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ corresponding|corresponding|JJ|_ genomes|genome|NNS|_ as|as|IN|_ a|a|DT|_ service|service|NN|_ provided|provide|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -LRB-|-lrb-|-LRB-|_ www.vertis-biotech.com|www.vertis-biotech.com|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ This|this|DT|_ involved|involved|JJ|_ trimming|trim|VBG|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ masking|mask|VBG|_ for|for|IN|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ .|.|.|_
For|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4|4|CD|_ libraries|library|NNS|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ bacterial|bacterial|JJ|_ samples|sample|NNS|_ x|x|CC|_ 2|2|CD|_ treatments|treatment|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ we|we|PRP|_ counted|count|VBD|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ times|time|NNS|_ each|each|DT|_ nucleotide|nucleotide|NN|_ position|position|NN|_ was|be|VBD|_ the|the|DT|_ first|first|JJ|_ in|in|IN|_ a|a|DT|_ sequence|sequence|NN|_ read|read|VBN|_ using|use|VBG|_ a|a|DT|_ simple|simple|JJ|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ unpubl|unpubl|NN|_ .|.|.|_ resource|resource|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ were|be|VBD|_ then|then|RB|_ processed|process|VBN|_ separately|separately|RB|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ The|the|DT|_ reference|reference|NN|_ genomes|genome|NNS|_ used|use|VBN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ strain|strain|NN|_ BW25113|bw25113|NN|_ and|and|CC|_ S.|S.|NNP|_ coelicolor|coelicolor|VBP|_ A3|a3|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ M145|m145|NN|_ were|be|VBD|_ U00096|u00096|NN|_ .2|.2|NN|_ and|and|CC|_ AL645882|al645882|NN|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BedGraphs|bedgraph|NNS|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ TAP|tap|NN|_ treatment|treatment|NN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ Separate|separate|JJ|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ pellet|pellet|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ using|use|VBG|_ a|a|DT|_ well-established|well-established|JJ|_ ,|,|,|_ published|publish|VBN|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ .|.|.|_ In|in|IN|_ RNA|rna|NN|_ Turnover|turnover|NN|_ in|in|IN|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Archaea|Archaea|NNP|_ and|and|CC|_ Organelles|Organelles|NNP|_ ,|,|,|_ Vol|Vol|NNP|_ 447|447|CD|_ -LRB-|-lrb-|-LRB-|_ ed|ed|VBN|_ .|.|.|_ LE|LE|NNP|_ Maquat|Maquat|NNP|_ ,|,|,|_ CM|cm|NN|_ Arraiano|arraiano|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pp.|pp.|NN|_ 215|215|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ of|of|IN|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ Kirby|Kirby|NNP|_ mix|mix|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ .|.|.|_ Practical|Practical|NNP|_ Streptomyces|Streptomyces|NNP|_ Genetics|Genetics|NNP|_ .|.|.|_ The|the|DT|_ John|John|NNP|_ Innes|Innes|NNP|_ Foundation|Foundation|NNP|_ ,|,|,|_ Norwich|Norwich|NNP|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ µL|µl|NN|_ per|per|IN|_ 1|1|CD|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ unit|unit|NN|_ ,|,|,|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ Lysing|lyse|VBG|_ Matrix|Matrix|NNP|_ B|B|NNP|_ tubes|tube|NNS|_ containing|contain|VBG|_ fine|fine|JJ|_ silica|silica|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ high-speed|high-speed|JJ|_ benchtop|benchtop|NN|_ homogenizer|homogenizer|NN|_ -LRB-|-lrb-|-LRB-|_ Fastprep-24|fastprep-24|NN|_ ,|,|,|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ;|;|:|_ set|set|VBN|_ at|at|IN|_ 6.5|6.5|CD|_ M/s|m/s|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ three|three|CD|_ cycles|cycle|NNS|_ of|of|IN|_ homogenisation|homogenisation|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ with|with|IN|_ cooling|cooling|NN|_ between|between|IN|_ each|each|DT|_ cycle|cycle|NN|_ in|in|IN|_ an|a|DT|_ ice-water|ice-water|JJ|_ bath|bath|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ lysates|lysate|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ acidic|acidic|JJ|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ :|:|:|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ :|:|:|_ 50|50|CD|_ :|:|:|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ chloroform|chloroform|NN|_ :|:|:|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -LRB-|-lrb-|-LRB-|_ 49|49|CD|_ :|:|:|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Nucleic|nucleic|JJ|_ acid|acid|NN|_ in|in|IN|_ the|the|DT|_ aqueous|aqueous|JJ|_ phase|phase|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ adding|add|VBG|_ NaCl|nacl|NN|_ to|to|TO|_ 150|150|CD|_ mM|mm|NN|KWSUPP and|and|CC|_ 2.5|2.5|CD|_ x|x|CC|_ volumes|volume|NNS|_ of|of|IN|_ 100|100|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ ethanol|ethanol|NN|_ ,|,|,|_ chilling|chill|VBG|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 13,000|13,000|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ nucleic|nucleic|JJ|_ acid|acid|NN|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ 700|700|CD|_ µL|µl|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ ethanol|ethanol|NN|_ ,|,|,|_ air|air|NN|_ dried|dry|VBD|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNase-free|rnase-free|JJ|_ water|water|NN|_ .|.|.|_ Contaminating|contaminate|VBG|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ both|both|DT|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ S.|s.|FW|_ coelicolor|coelicolor|FW|_ by|by|IN|_ incubating|incubate|VBG|_ with|with|IN|_ DNase|dnase|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ the|the|DT|_ vendor|vendor|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ a|a|DT|_ NanoDropTM|nanodroptm|NN|_ 1000|1000|CD|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ -LRB-|-lrb-|-LRB-|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ enriched|enrich|VBN|_ for|for|IN|_ mRNA|mrna|NN|_ using|use|VBG|_ MICROBExpress-Bacteria|microbexpress-bacteria|JJ|_ beads|bead|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -LRB-|-lrb-|-LRB-|_ www.vertis-biotech.com|www.vertis-biotech.com|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ a|a|DT|_ service|service|NN|_ that|that|WDT|_ included|include|VBD|_ treating|treat|VBG|_ an|a|DT|_ aliquot|aliquot|NN|_ of|of|IN|_ each|each|DT|_ RNA|rna|NN|_ sample|sample|NN|_ with|with|IN|_ TAP|tap|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ sequencing|sequencing|NN|_ adaptor|adaptor|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ transcripts|transcript|NNS|_ prior|prior|RB|_ to|to|TO|_ fragmentation|fragmentation|NN|_ ,|,|,|_ thereby|thereby|RB|_ allowing|allow|VBG|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ both|both|DT|_ long|long|JJ|_ and|and|CC|_ short|short|JJ|_ transcripts|transcript|NNS|_ to|to|TO|_ be|be|VB|_ detected|detect|VBN|_ .|.|.|_ Each|each|DT|_ of|of|IN|_ the|the|DT|_ 4|4|CD|_ libraries|library|NNS|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ a|a|DT|_ different|different|JJ|_ barcode|barcode|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ strain|strain|NN|_ BW25113|bw25113|NN|_ -LRB-|-lrb-|-LRB-|_ Datsenko|Datsenko|NNP|_ &|&|CC|_ Wanner|Wanner|NNP|_ 2000|2000|CD|_ .|.|.|_ PNAS|PNAS|NNP|_ 97|97|CD|_ :|:|:|_ 6640|6640|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ cultivated|cultivate|VBN|_ in|in|IN|_ 100|100|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ 1972|1972|CD|_ .|.|.|_ In|in|IN|_ :|:|:|_ Experiments|experiment|NNS|_ in|in|IN|_ molecular|molecular|JJ|_ genetics|genetics|NNS|_ .|.|.|_ Cold|Cold|NNP|_ Spring|Spring|NNP|_ Harbor|Harbor|NNP|_ Laboratory|Laboratory|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ mL|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ an|a|DT|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ 0.6|0.6|CD|_ .|.|.|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ A3|a3|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ M145|m145|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ .|.|.|_ Practical|Practical|NNP|_ Streptomyces|Streptomyces|NNP|_ Genetics|Genetics|NNP|_ .|.|.|_ The|the|DT|_ John|John|NNP|_ Innes|Innes|NNP|_ Foundation|Foundation|NNP|_ ,|,|,|_ Norwich|Norwich|NNP|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ YEME|yeme|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ the|the|DT|_ mycelia|mycelia|NN|_ became|become|VBD|_ pigmented|pigmented|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
E.|e.|FW|_ coli|coli|FW|_ batch|batch|NN|_ culture|culture|NN|_ with|with|IN|_ TAP|tap|NN|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ ,|,|,|_ a|a|DT|_ one-eighth|one-eighth|NN|_ volume|volume|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ ethanol|ethanol|NN|_ ;|;|:|_ 5|5|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ culture|culture|NN|_ to|to|TO|_ inhibit|inhibit|VB|_ cell|cell|NN|_ metabolism|metabolism|NN|_ -LRB-|-lrb-|-LRB-|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ .|.|.|_ In|in|IN|_ RNA|rna|NN|_ Turnover|turnover|NN|_ in|in|IN|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Archaea|Archaea|NNP|_ and|and|CC|_ Organelles|Organelles|NNP|_ ,|,|,|_ Vol|Vol|NNP|_ 447|447|CD|_ -LRB-|-lrb-|-LRB-|_ ed|ed|VBN|_ .|.|.|_ LE|LE|NNP|_ Maquat|Maquat|NNP|_ ,|,|,|_ CM|cm|NN|_ Arraiano|arraiano|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pp.|pp.|NN|_ 215|215|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ When|when|WRB|_ necessary|necessary|JJ|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype|genotype|NN|_ :|:|:|_ wild-type|wild-type|JJ|_
treatment|treatment|NN|_ :|:|:|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ strain|strain|NN|_ BW25113|bw25113|NN|_ -LRB-|-lrb-|-LRB-|_ Datsenko|Datsenko|NNP|_ &|&|CC|_ Wanner|Wanner|NNP|_ 2000|2000|CD|_ .|.|.|_ PNAS|PNAS|NNP|_ 97|97|CD|_ :|:|:|_ 6640|6640|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ cultivated|cultivate|VBN|_ in|in|IN|_ 100|100|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ 1972|1972|CD|_ .|.|.|_ In|in|IN|_ :|:|:|_ Experiments|experiment|NNS|_ in|in|IN|_ molecular|molecular|JJ|_ genetics|genetics|NNS|_ .|.|.|_ Cold|Cold|NNP|_ Spring|Spring|NNP|_ Harbor|Harbor|NNP|_ Laboratory|Laboratory|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ mL|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ an|a|DT|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ 0.6|0.6|CD|_ .|.|.|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ A3|a3|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ M145|m145|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ .|.|.|_ Practical|Practical|NNP|_ Streptomyces|Streptomyces|NNP|_ Genetics|Genetics|NNP|_ .|.|.|_ The|the|DT|_ John|John|NNP|_ Innes|Innes|NNP|_ Foundation|Foundation|NNP|_ ,|,|,|_ Norwich|Norwich|NNP|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ YEME|yeme|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ the|the|DT|_ mycelia|mycelia|NN|_ became|become|VBD|_ pigmented|pigmented|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
E.|e.|FW|_ coli|coli|FW|_ batch|batch|NN|_ culture|culture|NN|_ with|with|IN|_ TAP|tap|NN|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ ,|,|,|_ a|a|DT|_ one-eighth|one-eighth|NN|_ volume|volume|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ ethanol|ethanol|NN|_ ;|;|:|_ 5|5|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v/v|v/v|NN|_ -RSB-|-rsb-|-RRB-|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ culture|culture|NN|_ to|to|TO|_ inhibit|inhibit|VB|_ cell|cell|NN|_ metabolism|metabolism|NN|_ -LRB-|-lrb-|-LRB-|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ .|.|.|_ In|in|IN|_ RNA|rna|NN|_ Turnover|turnover|NN|_ in|in|IN|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Archaea|Archaea|NNP|_ and|and|CC|_ Organelles|Organelles|NNP|_ ,|,|,|_ Vol|Vol|NNP|_ 447|447|CD|_ -LRB-|-lrb-|-LRB-|_ ed|ed|VBN|_ .|.|.|_ LE|LE|NNP|_ Maquat|Maquat|NNP|_ ,|,|,|_ CM|cm|NN|_ Arraiano|arraiano|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pp.|pp.|NN|_ 215|215|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ When|when|WRB|_ necessary|necessary|JJ|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_
David|David|NNP|_ ,|,|,|_ ,|,|,|_ Romero|Romero|NNP|_ A.|A.|NNP|_
The|The|NNP|_ amplified|amplify|VBD|_ cDNA|cdna|NN|_ libraries|library|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ .|.|.|_ Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_ Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_
Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913/ASM584v1|000913/asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ counts|count|NNS|_
Total|Total|NNP|_ mRNA|mrna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ each|each|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Terminator|Terminator|NNP|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Phosphate|phosphate|NN|_ Dependent|dependent|JJ|_ Exonuclease|exonuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ enrich|enrich|VB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tri-phosphorylated|tri-phosphorylated|JJ|_ mRNAs|mrna|NNS|_ .|.|.|_ Intact|intact|JJ|_ tri-phosphorylated|tri-phosphorylated|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNA|rna|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ Polyphosphatase|polyphosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|VB|_ monophosphorylated|monophosphorylate|VBN|_ RNA|rna|NN|_ for|for|IN|_ ligation|ligation|NN|_ to|to|TO|_ RNA|rna|NN|_ adaptors|adaptor|NNS|_ .|.|.|_ cDNAs|cdna|NNS|_ were|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ the|the|DT|_ adaptor-ligated|adaptor-ligated|JJ|_ mRNAs|mrna|NNS|_ as|as|IN|_ template|template|NN|_ using|use|VBG|_ a|a|DT|_ modified|modify|VBN|_ small|small|JJ|_ RNA|rna|NN|_ RT|rt|NN|_ primer|primer|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ and|and|CC|_ Superscript|Superscript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ samples|sample|NNS|_ were|be|VBD|_ amplified|amplify|VBN|_ ,|,|,|_ and|and|CC|_ size|size|NN|_ fractionated|fractionate|VBN|_ from|from|IN|_ 100|100|CD|_ to|to|TO|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP media|media|NNS|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
treatment|treatment|NN|_ :|:|:|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP media|media|NNS|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ amplified|amplify|VBD|_ cDNA|cdna|NN|_ libraries|library|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ .|.|.|_ Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_ Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_
Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913/ASM584v1|000913/asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ counts|count|NNS|_
Total|Total|NNP|_ mRNA|mrna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ each|each|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Terminator|Terminator|NNP|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Phosphate|phosphate|NN|_ Dependent|dependent|JJ|_ Exonuclease|exonuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ enrich|enrich|VB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tri-phosphorylated|tri-phosphorylated|JJ|_ mRNAs|mrna|NNS|_ .|.|.|_ Intact|intact|JJ|_ tri-phosphorylated|tri-phosphorylated|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNA|rna|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ Polyphosphatase|polyphosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|VB|_ monophosphorylated|monophosphorylate|VBN|_ RNA|rna|NN|_ for|for|IN|_ ligation|ligation|NN|_ to|to|TO|_ RNA|rna|NN|_ adaptors|adaptor|NNS|_ .|.|.|_ cDNAs|cdna|NNS|_ were|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ the|the|DT|_ adaptor-ligated|adaptor-ligated|JJ|_ mRNAs|mrna|NNS|_ as|as|IN|_ template|template|NN|_ using|use|VBG|_ a|a|DT|_ modified|modify|VBN|_ small|small|JJ|_ RNA|rna|NN|_ RT|rt|NN|_ primer|primer|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ and|and|CC|_ Superscript|Superscript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ samples|sample|NNS|_ were|be|VBD|_ amplified|amplify|VBN|_ ,|,|,|_ and|and|CC|_ size|size|NN|_ fractionated|fractionate|VBN|_ from|from|IN|_ 100|100|CD|_ to|to|TO|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ W2|w2|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
treatment|treatment|NN|_ :|:|:|_ glutamine|glutamine|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ W2|w2|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ amplified|amplify|VBD|_ cDNA|cdna|NN|_ libraries|library|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ .|.|.|_ Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_ Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_
Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913/ASM584v1|000913/asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ counts|count|NNS|_
Total|Total|NNP|_ mRNA|mrna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ each|each|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Terminator|Terminator|NNP|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Phosphate|phosphate|NN|_ Dependent|dependent|JJ|_ Exonuclease|exonuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ enrich|enrich|VB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tri-phosphorylated|tri-phosphorylated|JJ|_ mRNAs|mrna|NNS|_ .|.|.|_ Intact|intact|JJ|_ tri-phosphorylated|tri-phosphorylated|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNA|rna|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ Polyphosphatase|polyphosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|VB|_ monophosphorylated|monophosphorylate|VBN|_ RNA|rna|NN|_ for|for|IN|_ ligation|ligation|NN|_ to|to|TO|_ RNA|rna|NN|_ adaptors|adaptor|NNS|_ .|.|.|_ cDNAs|cdna|NNS|_ were|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ the|the|DT|_ adaptor-ligated|adaptor-ligated|JJ|_ mRNAs|mrna|NNS|_ as|as|IN|_ template|template|NN|_ using|use|VBG|_ a|a|DT|_ modified|modify|VBN|_ small|small|JJ|_ RNA|rna|NN|_ RT|rt|NN|_ primer|primer|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ and|and|CC|_ Superscript|Superscript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ samples|sample|NNS|_ were|be|VBD|_ amplified|amplify|VBN|_ ,|,|,|_ and|and|CC|_ size|size|NN|_ fractionated|fractionate|VBN|_ from|from|IN|_ 100|100|CD|_ to|to|TO|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ W2|w2|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
treatment|treatment|NN|_ :|:|:|_ glutamine|glutamine|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ W2|w2|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ amplified|amplify|VBD|_ cDNA|cdna|NN|_ libraries|library|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ .|.|.|_ Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_ Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_
Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913/ASM584v1|000913/asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ counts|count|NNS|_
Total|Total|NNP|_ mRNA|mrna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ each|each|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Terminator|Terminator|NNP|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Phosphate|phosphate|NN|_ Dependent|dependent|JJ|_ Exonuclease|exonuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ enrich|enrich|VB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tri-phosphorylated|tri-phosphorylated|JJ|_ mRNAs|mrna|NNS|_ .|.|.|_ Intact|intact|JJ|_ tri-phosphorylated|tri-phosphorylated|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNA|rna|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ Polyphosphatase|polyphosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|VB|_ monophosphorylated|monophosphorylate|VBN|_ RNA|rna|NN|_ for|for|IN|_ ligation|ligation|NN|_ to|to|TO|_ RNA|rna|NN|_ adaptors|adaptor|NNS|_ .|.|.|_ cDNAs|cdna|NNS|_ were|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ the|the|DT|_ adaptor-ligated|adaptor-ligated|JJ|_ mRNAs|mrna|NNS|_ as|as|IN|_ template|template|NN|_ using|use|VBG|_ a|a|DT|_ modified|modify|VBN|_ small|small|JJ|_ RNA|rna|NN|_ RT|rt|NN|_ primer|primer|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ and|and|CC|_ Superscript|Superscript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ samples|sample|NNS|_ were|be|VBD|_ amplified|amplify|VBN|_ ,|,|,|_ and|and|CC|_ size|size|NN|_ fractionated|fractionate|VBN|_ from|from|IN|_ 100|100|CD|_ to|to|TO|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ media|media|NNS|_ ,|,|,|_ with|with|IN|_ 42oC|42oc|NN|_ heatshock|heatshock|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
treatment|treatment|NN|_ :|:|:|_ heat|heat|NN|_ shock|shock|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ media|media|NNS|_ ,|,|,|_ with|with|IN|_ 42oC|42oc|NN|_ heatshock|heatshock|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
The|The|NNP|_ amplified|amplify|VBD|_ cDNA|cdna|NN|_ libraries|library|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ .|.|.|_ Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_ Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_
Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913/ASM584v1|000913/asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ counts|count|NNS|_
Total|Total|NNP|_ mRNA|mrna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ each|each|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Terminator|Terminator|NNP|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Phosphate|phosphate|NN|_ Dependent|dependent|JJ|_ Exonuclease|exonuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ enrich|enrich|VB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tri-phosphorylated|tri-phosphorylated|JJ|_ mRNAs|mrna|NNS|_ .|.|.|_ Intact|intact|JJ|_ tri-phosphorylated|tri-phosphorylated|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNA|rna|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ Polyphosphatase|polyphosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|VB|_ monophosphorylated|monophosphorylate|VBN|_ RNA|rna|NN|_ for|for|IN|_ ligation|ligation|NN|_ to|to|TO|_ RNA|rna|NN|_ adaptors|adaptor|NNS|_ .|.|.|_ cDNAs|cdna|NNS|_ were|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ the|the|DT|_ adaptor-ligated|adaptor-ligated|JJ|_ mRNAs|mrna|NNS|_ as|as|IN|_ template|template|NN|_ using|use|VBG|_ a|a|DT|_ modified|modify|VBN|_ small|small|JJ|_ RNA|rna|NN|_ RT|rt|NN|_ primer|primer|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ and|and|CC|_ Superscript|Superscript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ samples|sample|NNS|_ were|be|VBD|_ amplified|amplify|VBN|_ ,|,|,|_ and|and|CC|_ size|size|NN|_ fractionated|fractionate|VBN|_ from|from|IN|_ 100|100|CD|_ to|to|TO|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ media|media|NNS|_ ,|,|,|_ with|with|IN|_ 42oC|42oc|NN|_ heatshock|heatshock|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
treatment|treatment|NN|_ :|:|:|_ heat|heat|NN|_ shock|shock|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ media|media|NNS|_ ,|,|,|_ with|with|IN|_ 42oC|42oc|NN|_ heatshock|heatshock|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS15min|hs15min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ Heatshock|Heatshock|NNP|_ 15|15|CD|_ min|min|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS15min|hs15min|NN|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS15min|hs15min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ Heatshock|Heatshock|NNP|_ 15|15|CD|_ min|min|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS15min|hs15min|NN|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS30min|hs30min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ Heatshock|heatshock|NN|_ 30|30|CD|_ min|min|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS30min|hs30min|NN|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS30min|hs30min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ Heatshock|heatshock|NN|_ 30|30|CD|_ min|min|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS30min|hs30min|NN|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS60min|hs60min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ Heatshock|heatshock|NN|_ 60|60|CD|_ min|min|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS60min|hs60min|NN|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS60min|hs60min|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ Heatshock|heatshock|NN|_ 60|60|CD|_ min|min|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS60min|hs60min|NN|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P0h|m-p0h|JJ|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ MOPS-P|mops-p|NN|_ 0h|0h|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P0h|m-p0h|JJ|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P0h|m-p0h|JJ|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ MOPS-P|mops-p|NN|_ 0h|0h|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P0h|m-p0h|JJ|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P2h|m-p2h|JJ|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ MOPS-P|mops-p|NN|_ 2h|2h|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P2h|m-p2h|JJ|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P2h|m-p2h|JJ|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ MOPS-P|mops-p|NN|_ 2h|2h|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P2h|m-p2h|JJ|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P4h|m-p4h|JJ|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ MOPS-P|mops-p|NN|_ 4h|4h|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P4h|m-p4h|JJ|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P4h|m-p4h|JJ|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
culture/growth|culture/growth|NN|_ condition|condition|NN|_ :|:|:|_ MOPS-P|mops-p|NN|_ 4h|4h|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ M-P4h|m-p4h|JJ|_
Zhengchang|zhengchang|NN|_ ,|,|,|_ ,|,|,|_ Su|su|FW|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|JJ|_ WT|wt|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ ;|;|:|_ MG1655|mg1655|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|JJ|_ WT|wt|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|JJ|_ WT|wt|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ ;|;|:|_ MG1655|mg1655|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|JJ|_ WT|wt|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|JJ|_ WT|wt|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ ;|;|:|_ MG1655|mg1655|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|JJ|_ WT|wt|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|NN|_ +|+|CC|_ ade|ade|NN|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ ;|;|:|_ MG1655|mg1655|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ adenine|adenine|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|NN|_ +|+|CC|_ ade|ade|NN|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|NN|_ +|+|CC|_ L-trp|l-trp|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ ;|;|:|_ MG1655|mg1655|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ L-tryptophan|l-tryptophan|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ mg/L|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|NN|_ +|+|CC|_ L-trp|l-trp|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|SYM|_ -|-|:|_ O2|o2|CD|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ ;|;|:|_ MG1655|mg1655|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ anaerobic|anaerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|SYM|_ -|-|:|_ O2|o2|CD|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|SYM|_ -|-|:|_ O2|o2|CD|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ ;|;|:|_ MG1655|mg1655|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ anaerobic|anaerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|SYM|_ -|-|:|_ O2|o2|CD|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|SYM|_ -|-|:|_ O2|o2|CD|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ ;|;|:|_ MG1655|mg1655|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ anaerobic|anaerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
WT|wt|SYM|_ -|-|:|_ O2|o2|CD|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
nac|nac|NN|GEN KO|ko|NN|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ nac|nac|NN|GEN KO|ko|NN|_ ;|;|:|_ BW25113|bw25113|NN|_ Dnac|dnac|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
nac|nac|NN|GEN KO|ko|NN|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
nac|nac|NN|GEN KO|ko|NN|_ +|+|CC|_ ade|ade|NN|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ nac|nac|NN|GEN KO|ko|NN|_ ;|;|:|_ BW25113|bw25113|NN|_ Dnac|dnac|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ adenine|adenine|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
nac|nac|NN|GEN KO|ko|NN|_ +|+|CC|_ ade|ade|NN|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
cra|cra|NN|GEN KO|KO|NNP|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ cra|cra|NN|GEN KO|ko|NN|_ ;|;|:|_ BW25113|bw25113|NN|_ Dcra|dcra|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
cra|cra|NN|GEN KO|KO|NNP|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
cra|cra|NN|GEN KO|ko|NN|_ +|+|CC|_ L-trp|l-trp|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ cra|cra|NN|GEN KO|ko|NN|_ ;|;|:|_ BW25113|bw25113|NN|_ Dcra|dcra|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ L-tryptophan|l-tryptophan|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ mg/L|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
cra|cra|NN|GEN KO|ko|NN|_ +|+|CC|_ L-trp|l-trp|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
mntR|mntr|NN|GEN KO|KO|NNP|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ mntR|mntr|NN|GEN KO|ko|NN|_ ;|;|:|_ BW25113|bw25113|NN|_ DmntR|dmntr|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
mntR|mntr|NN|GEN KO|KO|NNP|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
mntR|mntr|NN|GEN KO|ko|SYM|_ -|-|:|_ O2|o2|CD|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ mntR|mntr|NN|GEN KO|ko|NN|_ ;|;|:|_ BW25113|bw25113|NN|_ DmntR|dmntr|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g/L|g/l|NN|_ glc|glc|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ media|media|NNS|_ -RRB-|-rrb-|-RRB-|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ anaerobic|anaerobic|JJ|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
mntR|mntr|NN|GEN KO|ko|SYM|_ -|-|:|_ O2|o2|CD|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Bernhard|Bernhard|NNP|_ ,|,|,|_ O|O|NNP|_ ,|,|,|_ Palsson|Palsson|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ complete|complete|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ version|version|NN|_ 2.0.5|2.0.5|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
ecoli|ecolus|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ count|count|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ manner|manner|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ McNulty|McNulty|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 22030749|22030749|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
23A1|23a1|NN|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ ydcR|ydcr|NN|GEN -LRB-|-lrb-|-LRB-|_ b1439|b1439|NN|_ -RRB-|-rrb-|-RRB-|_ MUTANT|mutant|JJ|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
23A1|23a1|NN|_
Kristof|Kristof|NNP|_ ,|,|,|_ ,|,|,|_ Engelen|Engelen|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ complete|complete|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ version|version|NN|_ 2.0.5|2.0.5|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
ecoli|ecolus|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ count|count|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ manner|manner|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ McNulty|McNulty|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 22030749|22030749|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
23B1|23b1|NN|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ ydcR|ydcr|NN|GEN -LRB-|-lrb-|-LRB-|_ b1439|b1439|NN|_ -RRB-|-rrb-|-RRB-|_ MUTANT|mutant|JJ|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
23B1|23b1|NN|_
Kristof|Kristof|NNP|_ ,|,|,|_ ,|,|,|_ Engelen|Engelen|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ complete|complete|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ version|version|NN|_ 2.0.5|2.0.5|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
ecoli|ecolus|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ count|count|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ manner|manner|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ McNulty|McNulty|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 22030749|22030749|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
23C3|23c3|NN|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ ydcR|ydcr|NN|GEN -LRB-|-lrb-|-LRB-|_ b1439|b1439|NN|_ -RRB-|-rrb-|-RRB-|_ MUTANT|mutant|JJ|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
23C3|23c3|NN|_
Kristof|Kristof|NNP|_ ,|,|,|_ ,|,|,|_ Engelen|Engelen|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ complete|complete|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ version|version|NN|_ 2.0.5|2.0.5|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
ecoli|ecolus|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ count|count|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ manner|manner|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ McNulty|McNulty|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 22030749|22030749|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
39A1|39a1|NN|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ yjiR|yjir|NN|GEN -LRB-|-lrb-|-LRB-|_ b4340|b4340|NN|_ -RRB-|-rrb-|-RRB-|_ MUTANT|mutant|JJ|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
39A1|39a1|NN|_
Kristof|Kristof|NNP|_ ,|,|,|_ ,|,|,|_ Engelen|Engelen|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ complete|complete|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ version|version|NN|_ 2.0.5|2.0.5|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
ecoli|ecolus|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ count|count|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ manner|manner|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ McNulty|McNulty|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 22030749|22030749|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
39B1|39b1|NN|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ yjiR|yjir|NN|GEN -LRB-|-lrb-|-LRB-|_ b4340|b4340|NN|_ -RRB-|-rrb-|-RRB-|_ MUTANT|mutant|JJ|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
39B1|39b1|NN|_
Kristof|Kristof|NNP|_ ,|,|,|_ ,|,|,|_ Engelen|Engelen|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ complete|complete|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ version|version|NN|_ 2.0.5|2.0.5|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
ecoli|ecolus|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ count|count|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ manner|manner|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ McNulty|McNulty|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 22030749|22030749|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
39C1|39c1|NN|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ yjiR|yjir|NN|GEN -LRB-|-lrb-|-LRB-|_ b4340|b4340|NN|_ -RRB-|-rrb-|-RRB-|_ MUTANT|mutant|JJ|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
39C1|39c1|NN|_
Kristof|Kristof|NNP|_ ,|,|,|_ ,|,|,|_ Engelen|Engelen|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ complete|complete|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ version|version|NN|_ 2.0.5|2.0.5|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
ecoli|ecolus|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ count|count|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ manner|manner|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ McNulty|McNulty|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 22030749|22030749|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
WTA1|wta1|NN|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
WTA1|wta1|NN|_
Kristof|Kristof|NNP|_ ,|,|,|_ ,|,|,|_ Engelen|Engelen|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ complete|complete|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ version|version|NN|_ 2.0.5|2.0.5|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
ecoli|ecolus|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ count|count|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ manner|manner|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ McNulty|McNulty|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 22030749|22030749|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
WTB1|wtb1|NN|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
WTB1|wtb1|NN|_
Kristof|Kristof|NNP|_ ,|,|,|_ ,|,|,|_ Engelen|Engelen|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ complete|complete|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ version|version|NN|_ 2.0.5|2.0.5|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
ecoli|ecolus|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ count|count|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ manner|manner|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ McNulty|McNulty|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 22030749|22030749|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
WTC3|wtc3|NN|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
WTC3|wtc3|NN|_
Kristof|Kristof|NNP|_ ,|,|,|_ ,|,|,|_ Engelen|Engelen|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E|E|NNP|_ coli|coli|NN|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E|e|NN|_ coli|coli|NN|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ The|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ the|the|DT|_ footprint|footprint|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ footprint|footprint|NN|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_ files|file|NNS|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ at|at|IN|_ 37C|37c|NN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4C|4c|NN|_ .|.|.|_
Ribosome|Ribosome|NNP|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ More|more|RBR|_ at|at|IN|_ G.W.|G.W.|NNP|_ Li|Li|NNP|_ ,|,|,|_ D.|D.|NNP|_ Burkhardt|Burkhardt|NNP|_ ,|,|,|_ C.A.|C.A.|NNP|_ Gross|Gross|NNP|_ ,|,|,|_ J.|J.|NNP|_ S.|S.|NNP|_ Weissman|Weissman|NNP|_ -LRB-|-lrb-|-LRB-|_ Cell|cell|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ either|either|CC|_ full|full|JJ|_ supplement|supplement|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ An|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 400-fold|400-fold|JJ|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ a|a|DT|_ 2.8-liter|2.8-liter|JJ|_ flask|flask|NN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ aeration|aeration|NN|_ -LRB-|-lrb-|-LRB-|_ 180|180|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ fully|fully|RB|_ supplemented|supplement|VBN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP media|media|NNS|_
All|all|DT|_ cultures|culture|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ either|either|CC|_ full|full|JJ|_ supplement|supplement|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ An|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 400-fold|400-fold|JJ|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ a|a|DT|_ 2.8-liter|2.8-liter|JJ|_ flask|flask|NN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ aeration|aeration|NN|_ -LRB-|-lrb-|-LRB-|_ 180|180|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_
Gene-Wei|Gene-Wei|NNP|_ ,|,|,|_ ,|,|,|_ Li|Li|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ 1.8|1.8|CD|_ software|software|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
S.|S.|NNP|_ pneumoniae|pneumoniae|FW|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ D39|d39|NN|_ whole|whole|JJ|_ genome|genome|NN|_ with|with|IN|_ Rockhopper|rockhopper|JJ|_ version|version|NN|_ 1.21|1.21|CD|_ ,|,|,|_ using|use|VBG|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_ E.|e.|FW|_ coli|coli|FW|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ K-12|k-12|NN|_ ,|,|,|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ whole|whole|JJ|_ genome|genome|NN|_ with|with|IN|_ Bowtie|bowtie|NN|_ 2|2|CD|_ ,|,|,|_ using|use|VBG|_ parameters|parameter|NNS|_ --|--|:|_ mixed|mixed|JJ|_ --|--|:|_ discordant|discordant|JJ|_ -|-|:|_ D|d|NN|_ 10|10|CD|_ -|-|:|_ R|r|NN|_ 2|2|CD|_ -|-|:|_ N|n|NN|_ 0|0|CD|_ -|-|:|_ L|l|NN|_ 22|22|CD|_ -|-|:|_ i|i|FW|_ S|s|NN|_ ,0,2.50|,0,2.50|CD|_ .|.|.|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_ In|in|IN|_ short|short|RB|_ ,|,|,|_ exons|exon|NNS|_ from|from|IN|_ all|all|DT|_ isoforms|isoform|NNS|_ of|of|IN|_ a|a|DT|_ gene|gene|NN|_ were|be|VBD|_ merged|merge|VBN|_ to|to|TO|_ create|create|VB|_ one|one|CD|_ meta-transcript|meta-transcript|JJ|_ .|.|.|_ The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ falling|fall|VBG|_ in|in|IN|_ the|the|DT|_ exons|exon|NNS|_ of|of|IN|_ this|this|DT|_ meta-transcript|meta-transcript|JJ|_ were|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ the|the|DT|_ meta-transcript|meta-transcript|JJ|_ and|and|CC|_ by|by|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ the|the|DT|_ library|library|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ S.|S.|NNP|_ pneumoniae|pneumoniae|FW|_ samples|sample|NNS|_ this|this|DT|_ was|be|VBD|_ done|do|VBN|_ internally|internally|RB|_ by|by|IN|_ Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.21|1.21|CD|_ after|after|IN|_ aligning|align|VBG|_ reads|read|VBZ|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Streptococcus|streptococcus|NN|_ pneumoniae|pneumoniae|FW|_ D39|d39|NN|_ -LRB-|-lrb-|-LRB-|_ assembly|assembly|NN|_ ASM1436v1|asm1436v1|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ ,|,|,|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
For|for|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ ;|;|:|_ when|when|WRB|_ 1/3|1/3|CD|_ of|of|IN|_ the|the|DT|_ maximum|maximum|NN|_ OD600|od600|NN|_ was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 7,500|7,500|CD|_ rcf|rcf|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ frozen|freeze|VBN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ isolation|isolation|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ bead|bead|NN|_ beating|beating|NN|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ phenol-chloroform|phenol-chloroform|JJ|_ extractions|extraction|NNS|_ and|and|CC|_ ethanol|ethanol|NN|_ precipitations|precipitation|NNS|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ sample|sample|NN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ treatment|treatment|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ .|.|.|_ Ribolock|ribolock|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ avoid|avoid|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ following|follow|VBG|_ protocol|protocol|NN|_ :|:|:|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ first|first|JJ|_ treated|treat|VBN|_ with|with|IN|_ rDNase|rdnase|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ fragmented|fragmented|JJ|_ with|with|IN|_ ultrasound|ultrasound|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ pulses|pulse|NNS|_ of|of|IN|_ 30|30|CD|_ sec|sec|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Firststrand|Firststrand|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ primed|prime|VBN|_ with|with|IN|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 16-18|16-18|CD|_ cycles|cycle|NNS|_ ,|,|,|_ depending|depend|VBG|_ on|on|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ Aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ were|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ strain|strain|NN|_ JM83|jm83|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1/100|1/100|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ microtiter|microtiter|NN|_ plates|plate|NNS|_ .|.|.|_ To|to|TO|_ study|study|VB|_ the|the|DT|_ effects|effect|NNS|_ of|of|IN|_ trimethoprim|trimethoprim|NN|_ ,|,|,|_ cells|cell|NNS|_ grown|grow|VBN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ cells|cell|NNS|_ grown|grow|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ μg/ml|μg/ml|NN|_ trimethoprim|trimethoprim|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Untreated|untreated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ JM83|jm83|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ none|none|NN|_ -LRB-|-lrb-|-LRB-|_ untreated|untreated|JJ|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depleted|deplete|VBD|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ strain|strain|NN|_ JM83|jm83|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1/100|1/100|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ microtiter|microtiter|NN|_ plates|plate|NNS|_ .|.|.|_ To|to|TO|_ study|study|VB|_ the|the|DT|_ effects|effect|NNS|_ of|of|IN|_ trimethoprim|trimethoprim|NN|_ ,|,|,|_ cells|cell|NNS|_ grown|grow|VBN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ cells|cell|NNS|_ grown|grow|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ μg/ml|μg/ml|NN|_ trimethoprim|trimethoprim|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Untreated|untreated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_
Jelle|Jelle|NNP|_ ,|,|,|_ ,|,|,|_ Slager|Slager|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ 1.8|1.8|CD|_ software|software|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
S.|S.|NNP|_ pneumoniae|pneumoniae|FW|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ D39|d39|NN|_ whole|whole|JJ|_ genome|genome|NN|_ with|with|IN|_ Rockhopper|rockhopper|JJ|_ version|version|NN|_ 1.21|1.21|CD|_ ,|,|,|_ using|use|VBG|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_ E.|e.|FW|_ coli|coli|FW|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ K-12|k-12|NN|_ ,|,|,|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ whole|whole|JJ|_ genome|genome|NN|_ with|with|IN|_ Bowtie|bowtie|NN|_ 2|2|CD|_ ,|,|,|_ using|use|VBG|_ parameters|parameter|NNS|_ --|--|:|_ mixed|mixed|JJ|_ --|--|:|_ discordant|discordant|JJ|_ -|-|:|_ D|d|NN|_ 10|10|CD|_ -|-|:|_ R|r|NN|_ 2|2|CD|_ -|-|:|_ N|n|NN|_ 0|0|CD|_ -|-|:|_ L|l|NN|_ 22|22|CD|_ -|-|:|_ i|i|FW|_ S|s|NN|_ ,0,2.50|,0,2.50|CD|_ .|.|.|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_ In|in|IN|_ short|short|RB|_ ,|,|,|_ exons|exon|NNS|_ from|from|IN|_ all|all|DT|_ isoforms|isoform|NNS|_ of|of|IN|_ a|a|DT|_ gene|gene|NN|_ were|be|VBD|_ merged|merge|VBN|_ to|to|TO|_ create|create|VB|_ one|one|CD|_ meta-transcript|meta-transcript|JJ|_ .|.|.|_ The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ falling|fall|VBG|_ in|in|IN|_ the|the|DT|_ exons|exon|NNS|_ of|of|IN|_ this|this|DT|_ meta-transcript|meta-transcript|JJ|_ were|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ the|the|DT|_ meta-transcript|meta-transcript|JJ|_ and|and|CC|_ by|by|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ the|the|DT|_ library|library|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ S.|S.|NNP|_ pneumoniae|pneumoniae|FW|_ samples|sample|NNS|_ this|this|DT|_ was|be|VBD|_ done|do|VBN|_ internally|internally|RB|_ by|by|IN|_ Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.21|1.21|CD|_ after|after|IN|_ aligning|align|VBG|_ reads|read|VBZ|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Streptococcus|streptococcus|NN|_ pneumoniae|pneumoniae|FW|_ D39|d39|NN|_ -LRB-|-lrb-|-LRB-|_ assembly|assembly|NN|_ ASM1436v1|asm1436v1|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ ,|,|,|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
For|for|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ ;|;|:|_ when|when|WRB|_ 1/3|1/3|CD|_ of|of|IN|_ the|the|DT|_ maximum|maximum|NN|_ OD600|od600|NN|_ was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 7,500|7,500|CD|_ rcf|rcf|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ frozen|freeze|VBN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ isolation|isolation|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ bead|bead|NN|_ beating|beating|NN|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ phenol-chloroform|phenol-chloroform|JJ|_ extractions|extraction|NNS|_ and|and|CC|_ ethanol|ethanol|NN|_ precipitations|precipitation|NNS|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ sample|sample|NN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ treatment|treatment|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ .|.|.|_ Ribolock|ribolock|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ avoid|avoid|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ following|follow|VBG|_ protocol|protocol|NN|_ :|:|:|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ first|first|JJ|_ treated|treat|VBN|_ with|with|IN|_ rDNase|rdnase|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ fragmented|fragmented|JJ|_ with|with|IN|_ ultrasound|ultrasound|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ pulses|pulse|NNS|_ of|of|IN|_ 30|30|CD|_ sec|sec|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Firststrand|Firststrand|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ primed|prime|VBN|_ with|with|IN|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 16-18|16-18|CD|_ cycles|cycle|NNS|_ ,|,|,|_ depending|depend|VBG|_ on|on|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ Aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ were|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ strain|strain|NN|_ JM83|jm83|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1/100|1/100|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ microtiter|microtiter|NN|_ plates|plate|NNS|_ .|.|.|_ To|to|TO|_ study|study|VB|_ the|the|DT|_ effects|effect|NNS|_ of|of|IN|_ trimethoprim|trimethoprim|NN|_ ,|,|,|_ cells|cell|NNS|_ grown|grow|VBN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ cells|cell|NNS|_ grown|grow|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ μg/ml|μg/ml|NN|_ trimethoprim|trimethoprim|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Untreated|untreated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ JM83|jm83|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ none|none|NN|_ -LRB-|-lrb-|-LRB-|_ untreated|untreated|JJ|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depleted|deplete|VBD|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ strain|strain|NN|_ JM83|jm83|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1/100|1/100|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ microtiter|microtiter|NN|_ plates|plate|NNS|_ .|.|.|_ To|to|TO|_ study|study|VB|_ the|the|DT|_ effects|effect|NNS|_ of|of|IN|_ trimethoprim|trimethoprim|NN|_ ,|,|,|_ cells|cell|NNS|_ grown|grow|VBN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ cells|cell|NNS|_ grown|grow|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ μg/ml|μg/ml|NN|_ trimethoprim|trimethoprim|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Untreated|untreated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_
Jelle|Jelle|NNP|_ ,|,|,|_ ,|,|,|_ Slager|Slager|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ 1.8|1.8|CD|_ software|software|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
S.|S.|NNP|_ pneumoniae|pneumoniae|FW|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ D39|d39|NN|_ whole|whole|JJ|_ genome|genome|NN|_ with|with|IN|_ Rockhopper|rockhopper|JJ|_ version|version|NN|_ 1.21|1.21|CD|_ ,|,|,|_ using|use|VBG|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_ E.|e.|FW|_ coli|coli|FW|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ K-12|k-12|NN|_ ,|,|,|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ whole|whole|JJ|_ genome|genome|NN|_ with|with|IN|_ Bowtie|bowtie|NN|_ 2|2|CD|_ ,|,|,|_ using|use|VBG|_ parameters|parameter|NNS|_ --|--|:|_ mixed|mixed|JJ|_ --|--|:|_ discordant|discordant|JJ|_ -|-|:|_ D|d|NN|_ 10|10|CD|_ -|-|:|_ R|r|NN|_ 2|2|CD|_ -|-|:|_ N|n|NN|_ 0|0|CD|_ -|-|:|_ L|l|NN|_ 22|22|CD|_ -|-|:|_ i|i|FW|_ S|s|NN|_ ,0,2.50|,0,2.50|CD|_ .|.|.|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_ In|in|IN|_ short|short|RB|_ ,|,|,|_ exons|exon|NNS|_ from|from|IN|_ all|all|DT|_ isoforms|isoform|NNS|_ of|of|IN|_ a|a|DT|_ gene|gene|NN|_ were|be|VBD|_ merged|merge|VBN|_ to|to|TO|_ create|create|VB|_ one|one|CD|_ meta-transcript|meta-transcript|JJ|_ .|.|.|_ The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ falling|fall|VBG|_ in|in|IN|_ the|the|DT|_ exons|exon|NNS|_ of|of|IN|_ this|this|DT|_ meta-transcript|meta-transcript|JJ|_ were|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ the|the|DT|_ meta-transcript|meta-transcript|JJ|_ and|and|CC|_ by|by|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ the|the|DT|_ library|library|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ S.|S.|NNP|_ pneumoniae|pneumoniae|FW|_ samples|sample|NNS|_ this|this|DT|_ was|be|VBD|_ done|do|VBN|_ internally|internally|RB|_ by|by|IN|_ Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.21|1.21|CD|_ after|after|IN|_ aligning|align|VBG|_ reads|read|VBZ|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Streptococcus|streptococcus|NN|_ pneumoniae|pneumoniae|FW|_ D39|d39|NN|_ -LRB-|-lrb-|-LRB-|_ assembly|assembly|NN|_ ASM1436v1|asm1436v1|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ ,|,|,|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
For|for|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ ;|;|:|_ when|when|WRB|_ 1/3|1/3|CD|_ of|of|IN|_ the|the|DT|_ maximum|maximum|NN|_ OD600|od600|NN|_ was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 7,500|7,500|CD|_ rcf|rcf|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ frozen|freeze|VBN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ isolation|isolation|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ bead|bead|NN|_ beating|beating|NN|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ phenol-chloroform|phenol-chloroform|JJ|_ extractions|extraction|NNS|_ and|and|CC|_ ethanol|ethanol|NN|_ precipitations|precipitation|NNS|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ sample|sample|NN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ treatment|treatment|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ .|.|.|_ Ribolock|ribolock|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ avoid|avoid|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ following|follow|VBG|_ protocol|protocol|NN|_ :|:|:|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ first|first|JJ|_ treated|treat|VBN|_ with|with|IN|_ rDNase|rdnase|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ fragmented|fragmented|JJ|_ with|with|IN|_ ultrasound|ultrasound|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ pulses|pulse|NNS|_ of|of|IN|_ 30|30|CD|_ sec|sec|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Firststrand|Firststrand|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ primed|prime|VBN|_ with|with|IN|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 16-18|16-18|CD|_ cycles|cycle|NNS|_ ,|,|,|_ depending|depend|VBG|_ on|on|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ Aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ were|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ strain|strain|NN|_ JM83|jm83|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1/100|1/100|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ microtiter|microtiter|NN|_ plates|plate|NNS|_ .|.|.|_ To|to|TO|_ study|study|VB|_ the|the|DT|_ effects|effect|NNS|_ of|of|IN|_ trimethoprim|trimethoprim|NN|_ ,|,|,|_ cells|cell|NNS|_ grown|grow|VBN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ cells|cell|NNS|_ grown|grow|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ μg/ml|μg/ml|NN|_ trimethoprim|trimethoprim|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Trimethoprim-treated|trimethoprim-treated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ JM83|jm83|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 0.5|0.5|CD|_ μg/ml|μg/ml|NN|_ trimethoprim|trimethoprim|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depleted|deplete|VBD|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ strain|strain|NN|_ JM83|jm83|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1/100|1/100|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ microtiter|microtiter|NN|_ plates|plate|NNS|_ .|.|.|_ To|to|TO|_ study|study|VB|_ the|the|DT|_ effects|effect|NNS|_ of|of|IN|_ trimethoprim|trimethoprim|NN|_ ,|,|,|_ cells|cell|NNS|_ grown|grow|VBN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ cells|cell|NNS|_ grown|grow|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ μg/ml|μg/ml|NN|_ trimethoprim|trimethoprim|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Trimethoprim-treated|trimethoprim-treated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_
Jelle|Jelle|NNP|_ ,|,|,|_ ,|,|,|_ Slager|Slager|NNP|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ 1.8|1.8|CD|_ software|software|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
S.|S.|NNP|_ pneumoniae|pneumoniae|FW|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ D39|d39|NN|_ whole|whole|JJ|_ genome|genome|NN|_ with|with|IN|_ Rockhopper|rockhopper|JJ|_ version|version|NN|_ 1.21|1.21|CD|_ ,|,|,|_ using|use|VBG|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_ E.|e.|FW|_ coli|coli|FW|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ K-12|k-12|NN|_ ,|,|,|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ whole|whole|JJ|_ genome|genome|NN|_ with|with|IN|_ Bowtie|bowtie|NN|_ 2|2|CD|_ ,|,|,|_ using|use|VBG|_ parameters|parameter|NNS|_ --|--|:|_ mixed|mixed|JJ|_ --|--|:|_ discordant|discordant|JJ|_ -|-|:|_ D|d|NN|_ 10|10|CD|_ -|-|:|_ R|r|NN|_ 2|2|CD|_ -|-|:|_ N|n|NN|_ 0|0|CD|_ -|-|:|_ L|l|NN|_ 22|22|CD|_ -|-|:|_ i|i|FW|_ S|s|NN|_ ,0,2.50|,0,2.50|CD|_ .|.|.|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_ In|in|IN|_ short|short|RB|_ ,|,|,|_ exons|exon|NNS|_ from|from|IN|_ all|all|DT|_ isoforms|isoform|NNS|_ of|of|IN|_ a|a|DT|_ gene|gene|NN|_ were|be|VBD|_ merged|merge|VBN|_ to|to|TO|_ create|create|VB|_ one|one|CD|_ meta-transcript|meta-transcript|JJ|_ .|.|.|_ The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ falling|fall|VBG|_ in|in|IN|_ the|the|DT|_ exons|exon|NNS|_ of|of|IN|_ this|this|DT|_ meta-transcript|meta-transcript|JJ|_ were|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ the|the|DT|_ meta-transcript|meta-transcript|JJ|_ and|and|CC|_ by|by|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ the|the|DT|_ library|library|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ S.|S.|NNP|_ pneumoniae|pneumoniae|FW|_ samples|sample|NNS|_ this|this|DT|_ was|be|VBD|_ done|do|VBN|_ internally|internally|RB|_ by|by|IN|_ Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.21|1.21|CD|_ after|after|IN|_ aligning|align|VBG|_ reads|read|VBZ|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Streptococcus|streptococcus|NN|_ pneumoniae|pneumoniae|FW|_ D39|d39|NN|_ -LRB-|-lrb-|-LRB-|_ assembly|assembly|NN|_ ASM1436v1|asm1436v1|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ ,|,|,|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
For|for|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ ;|;|:|_ when|when|WRB|_ 1/3|1/3|CD|_ of|of|IN|_ the|the|DT|_ maximum|maximum|NN|_ OD600|od600|NN|_ was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 7,500|7,500|CD|_ rcf|rcf|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ frozen|freeze|VBN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ isolation|isolation|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ bead|bead|NN|_ beating|beating|NN|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ phenol-chloroform|phenol-chloroform|JJ|_ extractions|extraction|NNS|_ and|and|CC|_ ethanol|ethanol|NN|_ precipitations|precipitation|NNS|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ sample|sample|NN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ treatment|treatment|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ .|.|.|_ Ribolock|ribolock|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ avoid|avoid|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ following|follow|VBG|_ protocol|protocol|NN|_ :|:|:|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ first|first|JJ|_ treated|treat|VBN|_ with|with|IN|_ rDNase|rdnase|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ fragmented|fragmented|JJ|_ with|with|IN|_ ultrasound|ultrasound|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ pulses|pulse|NNS|_ of|of|IN|_ 30|30|CD|_ sec|sec|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Firststrand|Firststrand|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ primed|prime|VBN|_ with|with|IN|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 16-18|16-18|CD|_ cycles|cycle|NNS|_ ,|,|,|_ depending|depend|VBG|_ on|on|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ Aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ were|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ strain|strain|NN|_ JM83|jm83|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1/100|1/100|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ microtiter|microtiter|NN|_ plates|plate|NNS|_ .|.|.|_ To|to|TO|_ study|study|VB|_ the|the|DT|_ effects|effect|NNS|_ of|of|IN|_ trimethoprim|trimethoprim|NN|_ ,|,|,|_ cells|cell|NNS|_ grown|grow|VBN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ cells|cell|NNS|_ grown|grow|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ μg/ml|μg/ml|NN|_ trimethoprim|trimethoprim|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Trimethoprim-treated|trimethoprim-treated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ JM83|jm83|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 0.5|0.5|CD|_ μg/ml|μg/ml|NN|_ trimethoprim|trimethoprim|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depleted|deplete|VBD|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ strain|strain|NN|_ JM83|jm83|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1/100|1/100|CD|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ microtiter|microtiter|NN|_ plates|plate|NNS|_ .|.|.|_ To|to|TO|_ study|study|VB|_ the|the|DT|_ effects|effect|NNS|_ of|of|IN|_ trimethoprim|trimethoprim|NN|_ ,|,|,|_ cells|cell|NNS|_ grown|grow|VBN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ cells|cell|NNS|_ grown|grow|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ μg/ml|μg/ml|NN|_ trimethoprim|trimethoprim|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Trimethoprim-treated|trimethoprim-treated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_
Jelle|Jelle|NNP|_ ,|,|,|_ ,|,|,|_ Slager|Slager|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-delimited|comma-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
agent|agent|NN|_ :|:|:|_ Fe|Fe|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-delimited|comma-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
agent|agent|NN|_ :|:|:|_ Fe|Fe|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-delimited|comma-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
agent|agent|NN|_ :|:|:|_ DPD|dpd|NN|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-delimited|comma-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
agent|agent|NN|_ :|:|:|_ DPD|dpd|NN|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-delimited|comma-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ Δfur|Δfur|NNP|_
agent|agent|NN|_ :|:|:|_ Fe|Fe|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-delimited|comma-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ Δfur|Δfur|NNP|_
agent|agent|NN|_ :|:|:|_ Fe|Fe|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-delimited|comma-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ Δfur|Δfur|NNP|_
agent|agent|NN|_ :|:|:|_ DPD|dpd|NN|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-delimited|comma-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ Δfur|Δfur|NNP|_
agent|agent|NN|_ :|:|:|_ DPD|dpd|NN|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ M63|m63|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ M63|m63|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ M63|m63|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ M63|m63|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Demultiplexing|Demultiplexing|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng/μl|ng/μl|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ were|be|VBD|_ designed|design|VBN|_ for|for|IN|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ Illumina|Illumina|NNP|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
medium|medium|NN|_ :|:|:|_ M63|m63|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol/dry|ethanol/dry|NN|_ ice|ice|NN|_ slurry|slurry|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ could|could|MD|_ be|be|VB|_ extracted|extract|VBN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ no|no|DT|_ ethanol|ethanol|NN|_ exposure|exposure|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 70|70|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 70|70|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ no|no|DT|_ ethanol|ethanol|NN|_ exposure|exposure|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ no|no|DT|_ ethanol|ethanol|NN|_ exposure|exposure|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 70|70|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 70|70|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ no|no|DT|_ ethanol|ethanol|NN|_ exposure|exposure|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ no|no|DT|_ ethanol|ethanol|NN|_ exposure|exposure|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 70|70|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 70|70|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ no|no|DT|_ ethanol|ethanol|NN|_ exposure|exposure|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ no|no|DT|_ ethanol|ethanol|NN|_ exposure|exposure|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 70|70|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ genes|gene|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH/L|etoh/l|NN|_ ,|,|,|_ 70|70|CD|_ min|min|NN|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
Cultures|Cultures|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ vigorously|vigorously|RB|_ shaken|shake|VBN|_ -LRB-|-lrb-|-LRB-|_ 225|225|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ Fernbach|fernbach|NN|_ flasks|flask|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g/L|g/l|NN|_ once|once|RB|_ A600|a600|NN|_ of|of|IN|_ cultures|culture|NNS|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ prior|prior|RB|_ to|to|TO|_ ethanol|ethanol|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 70|70|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ T2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ rapidly|rapidly|RB|_ onto|onto|IN|_ 0.2|0.2|CD|_ µm|µm|NN|_ filters|filter|NNS|_ by|by|IN|_ vacuum|vacuum|NN|_ then|then|RB|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ arrest|arrest|VB|_ ribosomes|ribosome|NNS|_ .|.|.|_ Ribosome|ribosome|NN|_ footprinting|footprinting|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ digestion|digestion|NN|_ followed|follow|VBN|_ by|by|IN|_ monosome|monosome|JJ|_ isolation|isolation|NN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ .|.|.|_
Rembrandt|Rembrandt|NNP|_ ,|,|,|_ ,|,|,|_ Haft|Haft|NNP|_
Basecalls|Basecalls|NNPS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ .1.8|.1.8|CD|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ reads|read|VBZ|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 6.0.1|6.0.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ in|in|IN|_ tab|tab|NN|_ delimited|delimit|VBD|_ format|format|NN|_ .|.|.|_ Separate|separate|JJ|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ .|.|.|_ The|the|DT|_ start|start|NN|_ and|and|CC|_ end|end|NN|_ coordinates|coordinate|VBZ|_ should|should|MD|_ be|be|VB|_ the|the|DT|_ same|same|JJ|_ .|.|.|_ Each|each|DT|_ line|line|NN|_ in|in|IN|_ the|the|DT|_ data|data|NN|_ set|set|NN|_ represents|represent|VBZ|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ at|at|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ a|a|DT|_ sequence|sequence|NN|_ that|that|WDT|_ could|could|MD|_ be|be|VB|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ as|as|IN|_ desribed|desribe|VBN|_ in|in|IN|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2008|2008|CD|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
All|All|NNP|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cell|cell|NN|_ cultures|culture|NNS|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ N3433|n3433|NN|_
analysis|analysis|NN|_ :|:|:|_ in|in|FW|_ vivo|vivo|FW|_
genotype|genotype|NN|_ :|:|:|_ rne|rne|NN|GEN wild-type|wild-type|JJ|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ n/a|n/a|NN|_
All|all|DT|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cell|cell|NN|_ cultures|culture|NNS|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
Kenneth|Kenneth|NNP|_ ,|,|,|_ ,|,|,|_ McDowall|McDowall|NNP|_
Basecalls|Basecalls|NNPS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ .1.8|.1.8|CD|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ reads|read|VBZ|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 6.0.1|6.0.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ in|in|IN|_ tab|tab|NN|_ delimited|delimit|VBD|_ format|format|NN|_ .|.|.|_ Separate|separate|JJ|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ .|.|.|_ The|the|DT|_ start|start|NN|_ and|and|CC|_ end|end|NN|_ coordinates|coordinate|VBZ|_ should|should|MD|_ be|be|VB|_ the|the|DT|_ same|same|JJ|_ .|.|.|_ Each|each|DT|_ line|line|NN|_ in|in|IN|_ the|the|DT|_ data|data|NN|_ set|set|NN|_ represents|represent|VBZ|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ at|at|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ a|a|DT|_ sequence|sequence|NN|_ that|that|WDT|_ could|could|MD|_ be|be|VB|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ as|as|IN|_ desribed|desribe|VBN|_ in|in|IN|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2008|2008|CD|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
All|All|NNP|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cell|cell|NN|_ cultures|culture|NNS|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ N3431|n3431|NN|_
analysis|analysis|NN|_ :|:|:|_ in|in|FW|_ vivo|vivo|FW|_
genotype|genotype|NN|_ :|:|:|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ n/a|n/a|NN|_
All|all|DT|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cell|cell|NN|_ cultures|culture|NNS|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
Kenneth|Kenneth|NNP|_ ,|,|,|_ ,|,|,|_ McDowall|McDowall|NNP|_
Basecalls|Basecalls|NNPS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ .1.8|.1.8|CD|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ reads|read|VBZ|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 6.0.1|6.0.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ in|in|IN|_ tab|tab|NN|_ delimited|delimit|VBD|_ format|format|NN|_ .|.|.|_ Separate|separate|JJ|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ .|.|.|_ The|the|DT|_ start|start|NN|_ and|and|CC|_ end|end|NN|_ coordinates|coordinate|VBZ|_ should|should|MD|_ be|be|VB|_ the|the|DT|_ same|same|JJ|_ .|.|.|_ Each|each|DT|_ line|line|NN|_ in|in|IN|_ the|the|DT|_ data|data|NN|_ set|set|NN|_ represents|represent|VBZ|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ at|at|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ a|a|DT|_ sequence|sequence|NN|_ that|that|WDT|_ could|could|MD|_ be|be|VB|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ as|as|IN|_ desribed|desribe|VBN|_ in|in|IN|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2008|2008|CD|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
All|All|NNP|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cell|cell|NN|_ cultures|culture|NNS|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
analysis|analysis|NN|_ :|:|:|_ in|in|FW|_ vitro|vitro|FW|_
genotype|genotype|NN|_ :|:|:|_ n/a|n/a|NN|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
All|all|DT|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cell|cell|NN|_ cultures|culture|NNS|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
Kenneth|Kenneth|NNP|_ ,|,|,|_ ,|,|,|_ McDowall|McDowall|NNP|_
Basecalls|Basecalls|NNPS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ .1.8|.1.8|CD|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ reads|read|VBZ|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 6.0.1|6.0.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ in|in|IN|_ tab|tab|NN|_ delimited|delimit|VBD|_ format|format|NN|_ .|.|.|_ Separate|separate|JJ|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ .|.|.|_ The|the|DT|_ start|start|NN|_ and|and|CC|_ end|end|NN|_ coordinates|coordinate|VBZ|_ should|should|MD|_ be|be|VB|_ the|the|DT|_ same|same|JJ|_ .|.|.|_ Each|each|DT|_ line|line|NN|_ in|in|IN|_ the|the|DT|_ data|data|NN|_ set|set|NN|_ represents|represent|VBZ|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ at|at|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ a|a|DT|_ sequence|sequence|NN|_ that|that|WDT|_ could|could|MD|_ be|be|VB|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ as|as|IN|_ desribed|desribe|VBN|_ in|in|IN|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2008|2008|CD|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
All|All|NNP|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cell|cell|NN|_ cultures|culture|NNS|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
analysis|analysis|NN|_ :|:|:|_ in|in|FW|_ vitro|vitro|FW|_
genotype|genotype|NN|_ :|:|:|_ n/a|n/a|NN|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
All|all|DT|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cell|cell|NN|_ cultures|culture|NNS|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
Kenneth|Kenneth|NNP|_ ,|,|,|_ ,|,|,|_ McDowall|McDowall|NNP|_
Basecalls|Basecalls|NNPS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ .1.8|.1.8|CD|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ reads|read|VBZ|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 6.0.1|6.0.1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ in|in|IN|_ tab|tab|NN|_ delimited|delimit|VBD|_ format|format|NN|_ .|.|.|_ Separate|separate|JJ|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ .|.|.|_ The|the|DT|_ start|start|NN|_ and|and|CC|_ end|end|NN|_ coordinates|coordinate|VBZ|_ should|should|MD|_ be|be|VB|_ the|the|DT|_ same|same|JJ|_ .|.|.|_ Each|each|DT|_ line|line|NN|_ in|in|IN|_ the|the|DT|_ data|data|NN|_ set|set|NN|_ represents|represent|VBZ|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ at|at|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ a|a|DT|_ sequence|sequence|NN|_ that|that|WDT|_ could|could|MD|_ be|be|VB|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ as|as|IN|_ desribed|desribe|VBN|_ in|in|IN|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2008|2008|CD|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
All|All|NNP|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cell|cell|NN|_ cultures|culture|NNS|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GM11|gm11|NN|_
analysis|analysis|NN|_ :|:|:|_ in|in|FW|_ vivo|vivo|FW|_
genotype|genotype|NN|_ :|:|:|_ rng|rng|NN|GEN mutant|mutant|JJ|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ n/a|n/a|NN|_
All|all|DT|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ cell|cell|NN|_ cultures|culture|NNS|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
Kenneth|Kenneth|NNP|_ ,|,|,|_ ,|,|,|_ McDowall|McDowall|NNP|_
The|the|DT|_ data|datum|NNS|_ output|output|NN|_ from|from|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ Hiseq|Hiseq|NNP|_ System|System|NNP|_ was|be|VBD|_ obtained|obtain|VBN|_ directly|directly|RB|_ from|from|IN|_ Vertis|Vertis|NNP|_
For|for|IN|_ alignment|alignment|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ contained|contain|VBN|_ within|within|IN|_ the|the|DT|_ fastq|fastq|NN|_ files|file|VBZ|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ RefSeq|refseq|NN|_ NC|nc|NN|_ _|_|CD|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ short|short|JJ|_ read|read|NN|_ alignment|alignment|NN|_ tool|tool|NN|_ Bowtie2|bowtie2|NN|_ was|be|VBD|_ utilized|utilize|VBN|_ under|under|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_ Bowtie|Bowtie|NNP|_ parameters|parameter|NNS|_ were|be|VBD|_ set|set|VBN|_ to|to|TO|_ include|include|VB|_ only|only|RB|_ perfect|perfect|JJ|_ matches|match|NNS|_ and|and|CC|_ map|map|NN|GEN once|once|RB|_ reads|read|VBZ|_ that|that|IN|_ map|map|NN|GEN to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ genome|genome|NN|_ location|location|NN|_ ,|,|,|_ i.e.|i.e.|FW|_ ,|,|,|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ are|be|VBP|_ retained|retain|VBN|_ .|.|.|_ The|the|DT|_ output|output|NN|_ Bowtie2|bowtie2|NN|_ was|be|VBD|_ a|a|DT|_ SAM|SAM|NNP|_ files|file|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Used|use|VBD|_ SAMTOOLS|samtools|NN|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ PMID|pmid|NN|_ 1950593|1950593|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ sort|sort|VB|_ and|and|CC|_ index|index|NN|_ the|the|DT|_ SAM|SAM|NNP|_ files|file|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ Bowtie2|bowtie2|NN|_ and|and|CC|_ convert|convert|VB|_ them|they|PRP|_ to|to|TO|_ BAM|BAM|NNP|_ format|format|NN|_ .|.|.|_
Sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ processed|process|VBN|_ by|by|IN|_ conversion|conversion|NN|_ of|of|IN|_ the|the|DT|_ sample|sample|NN|_ alignment|alignment|NN|_ -LRB-|-lrb-|-LRB-|_ BAM|bam|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|VBZ|_ to|to|TO|_ strand-specific|strand-specific|JJ|_ base|base|NN|_ count|count|NN|_ -LRB-|-lrb-|-LRB-|_ BigWIG|bigwig|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ To|to|TO|_ accomplish|accomplish|VB|_ this|this|DT|_ an|a|DT|_ in-house|in-house|JJ|_ script|script|NN|_ was|be|VBD|_ created|create|VBN|_ to|to|TO|_ extract|extract|VB|_ strand-specific|strand-specific|JJ|_ base|base|NN|_ count|count|NN|_ data|datum|NNS|_ from|from|IN|_ BAM|BAM|NNP|_ files|file|NNS|_ -LRB-|-lrb-|-LRB-|_ outputs|output|NNS|_ are|be|VBP|_ positive|positive|JJ|_ and|and|CC|_ negative|negative|JJ|_ strand|strand|NN|_ BigWIG|bigwig|NN|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
BigWIG|bigwig|NN|_ files|file|NNS|_ were|be|VBD|_ viewed|view|VBN|_ and|and|CC|_ annotated|annotated|JJ|_ using|use|VBG|_ Jbrowse|Jbrowse|NNP|_ and|and|CC|_ Integrated|Integrated|NNP|_ Genome|Genome|NNP|_ Viewer|Viewer|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Reference|Reference|NNP|_ genome|genome|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ RefSeq|refseq|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWIG|bigwig|NN|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ showing|show|VBG|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ sequence|sequence|NN|_ reads|read|VBZ|_ .|.|.|_
All|All|NNP|_ samples|sample|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ extraction|extraction|NN|_ with|with|IN|_ DNA|dna|NN|_ digestion|digestion|NN|_ ,|,|,|_ following|follow|VBG|_ standard|standard|JJ|_ protocol|protocol|NN|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ at|at|IN|_ Vertis|Vertis|NNP|_ in|in|IN|_ Germany|Germany|NNP|_ using|use|VBG|_ a|a|DT|_ ligation|ligation|NN|_ based|base|VBN|_ stratagey|stratagey|NN|_ for|for|IN|_ Illumina|Illumina|NNP|_ whole|whole|JJ|_ transcriptome|transcriptome|NN|_ sequencing|sequencing|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ DNase|dnase|NN|_ I|i|CD|_ digested|digest|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ fragmented|fragment|VBN|_ by|by|IN|_ RNase|rnase|NN|_ III|iii|CD|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ labeled|label|VBN|_ as|as|IN|_ TEX|TEX|NNP|_ were|be|VBD|_ also|also|RB|_ subsequently|subsequently|RB|_ digested|digest|VBN|_ with|with|IN|_ Terminator|Terminator|NNP|_ Exonuclease|Exonuclease|NNP|_ -LRB-|-lrb-|-LRB-|_ TEX|TEX|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Pyrophosphate|pyrophosphate|NN|_ groups|group|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ ′|′|NN|_ terminus|terminus|NN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ an|a|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ ′|′|NN|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ BW38038|bw38038|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ BW39452|bw39452|NN|_ -LRB-|-lrb-|-LRB-|_ ΔrpoS|δrpos|NN|_ -RRB-|-rrb-|-RRB-|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP as|as|IN|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ pH|ph|NN|_ was|be|VBD|_ initially|initially|RB|_ 7.4|7.4|CD|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ agitation|agitation|NN|_ speed|speed|NN|_ was|be|VBD|_ 500|500|CD|_ rpm|rpm|NN|_ .|.|.|_ Culture|culture|NN|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ during|during|IN|_ logarithmic|logarithmic|JJ|_ growth|growth|NN|_ and|and|CC|_ following|follow|VBG|_ entry|entry|NN|_ into|into|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase for|for|IN|_ the|the|DT|_ WT|WT|NNP|_ and|and|CC|_ rpoS|rpos|NN|GEN mutant|mutant|NN|_ .|.|.|_ OD600|od600|CD|_ measurements|measurement|NNS|_ were|be|VBD|_ made|make|VBN|_ on|on|IN|_ a|a|DT|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ DU|DU|NNP|_ 800|800|CD|_ spectrophotometer|spectrophotometer|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ directly|directly|RB|_ into|into|IN|_ ice-cold|ice-cold|JJ|_ RNAlater|rnalater|NN|_ at|at|IN|_ a|a|DT|_ 1:1|1:1|CD|_ dilution|dilution|NN|_ to|to|TO|_ protect|protect|VB|_ RNA|rna|NN|_ from|from|IN|_ degradation|degradation|NN|_ and|and|CC|_ cells|cell|NNS|_ then|then|RB|_ were|be|VBD|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000rpm|8000rpm|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ RNAlater|rnalater|NN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW38028|bw38028|NN|_
Cell|cell|NN|_ culture|culture|NN|_
Prior|prior|RB|_ to|to|TO|_ total|total|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ harvested|harvest|VBN|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80.0|-80.0|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ RNAlater|rnalater|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW38028|bw38028|NN|_
genotype|genotype|NN|_ :|:|:|_ wt|wt|JJ|_
treatment|treatment|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_ sample|sample|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_ OD|od|NN|_ 0.4|0.4|CD|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ no|no|DT|_ RNA|rna|NN|_ treatment|treatment|NN|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ BW38038|bw38038|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ BW39452|bw39452|NN|_ -LRB-|-lrb-|-LRB-|_ ΔrpoS|δrpos|NN|_ -RRB-|-rrb-|-RRB-|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP as|as|IN|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ pH|ph|NN|_ was|be|VBD|_ initially|initially|RB|_ 7.4|7.4|CD|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ agitation|agitation|NN|_ speed|speed|NN|_ was|be|VBD|_ 500|500|CD|_ rpm|rpm|NN|_ .|.|.|_ Culture|culture|NN|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ during|during|IN|_ logarithmic|logarithmic|JJ|_ growth|growth|NN|_ and|and|CC|_ following|follow|VBG|_ entry|entry|NN|_ into|into|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase for|for|IN|_ the|the|DT|_ WT|WT|NNP|_ and|and|CC|_ rpoS|rpos|NN|GEN mutant|mutant|NN|_ .|.|.|_ OD600|od600|CD|_ measurements|measurement|NNS|_ were|be|VBD|_ made|make|VBN|_ on|on|IN|_ a|a|DT|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ DU|DU|NNP|_ 800|800|CD|_ spectrophotometer|spectrophotometer|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ directly|directly|RB|_ into|into|IN|_ ice-cold|ice-cold|JJ|_ RNAlater|rnalater|NN|_ at|at|IN|_ a|a|DT|_ 1:1|1:1|CD|_ dilution|dilution|NN|_ to|to|TO|_ protect|protect|VB|_ RNA|rna|NN|_ from|from|IN|_ degradation|degradation|NN|_ and|and|CC|_ cells|cell|NNS|_ then|then|RB|_ were|be|VBD|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000rpm|8000rpm|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ RNAlater|rnalater|NN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW38028|bw38028|NN|_
Cell|cell|NN|_ culture|culture|NN|_
Prior|prior|RB|_ to|to|TO|_ total|total|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ harvested|harvest|VBN|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80.0|-80.0|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ RNAlater|rnalater|NN|_ .|.|.|_
James|James|NNP|_ ,|,|,|_ ,|,|,|_ Creecy|Creecy|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E|E|NNP|_ coli|coli|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ 1|1|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ .|.|.|_ This|this|DT|_ allows|allow|VBZ|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reports|report|NNS|_ only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ align|align|NN|_ 1|1|CD|_ or|or|CC|_ fewer|fewer|JJR|_ times|time|NNS|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E|e|NN|_ coli|coli|NN|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ The|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ the|the|DT|_ footprint|footprint|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ footprint|footprint|NN|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_ files|file|NNS|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ at|at|IN|_ 37C|37c|NN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4C|4c|NN|_ .|.|.|_
Ribosome|Ribosome|NNP|_ protected|protect|VBD|_ and|and|CC|_ total|total|JJ|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ .|.|.|_ Fragments|fragment|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ More|more|JJR|_ details|detail|NNS|_ at|at|IN|_ MS|ms|NN|_ Guo|Guo|NNP|_ ,|,|,|_ TB|tb|NN|_ Updegrove|Updegrove|NNP|_ ,|,|,|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ Genes|gene|NNS|_ Dev|dev|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ fully|fully|RB|_ supplemented|supplement|VBN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD420|od420|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ 4|4|CD|_ subcultures|subculture|NNS|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ribosome|ribosome|NN|_ profiling|profiling|NN|_ in|in|IN|_ rich|rich|JJ|_ defined|define|VBN|_ media|media|NNS|_
At|at|IN|_ OD|od|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ length|length|NN|_ of|of|IN|_ time|time|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ fully|fully|RB|_ supplemented|supplement|VBN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP media|media|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ fully|fully|RB|_ supplemented|supplement|VBN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD420|od420|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ 4|4|CD|_ subcultures|subculture|NNS|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ribosome|ribosome|NN|_ profiling|profiling|NN|_ in|in|IN|_ rich|rich|JJ|_ defined|define|VBN|_ media|media|NNS|_
At|at|IN|_ OD|od|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ length|length|NN|_ of|of|IN|_ time|time|NN|_ .|.|.|_
Carol|Carol|NNP|_ ,|,|,|_ A|A|NNP|_ ,|,|,|_ Gross|Gross|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E|E|NNP|_ coli|coli|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ 1|1|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ .|.|.|_ This|this|DT|_ allows|allow|VBZ|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reports|report|NNS|_ only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ align|align|NN|_ 1|1|CD|_ or|or|CC|_ fewer|fewer|JJR|_ times|time|NNS|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E|e|NN|_ coli|coli|NN|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ The|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ the|the|DT|_ footprint|footprint|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ footprint|footprint|NN|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_ files|file|NNS|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ at|at|IN|_ 37C|37c|NN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4C|4c|NN|_ .|.|.|_
Ribosome|Ribosome|NNP|_ protected|protect|VBD|_ and|and|CC|_ total|total|JJ|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ .|.|.|_ Fragments|fragment|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ More|more|JJR|_ details|detail|NNS|_ at|at|IN|_ MS|ms|NN|_ Guo|Guo|NNP|_ ,|,|,|_ TB|tb|NN|_ Updegrove|Updegrove|NNP|_ ,|,|,|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ Genes|gene|NNS|_ Dev|dev|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ fully|fully|RB|_ supplemented|supplement|VBN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD420|od420|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ 4|4|CD|_ subcultures|subculture|NNS|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ribosome|ribosome|NN|_ profiling|profiling|NN|_ in|in|IN|_ rich|rich|JJ|_ defined|define|VBN|_ media|media|NNS|_
At|at|IN|_ OD|od|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ length|length|NN|_ of|of|IN|_ time|time|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
media|media|NNS|_ :|:|:|_ fully|fully|RB|_ supplemented|supplement|VBN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP media|media|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ fully|fully|RB|_ supplemented|supplement|VBN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD420|od420|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ 4|4|CD|_ subcultures|subculture|NNS|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ribosome|ribosome|NN|_ profiling|profiling|NN|_ in|in|IN|_ rich|rich|JJ|_ defined|define|VBN|_ media|media|NNS|_
At|at|IN|_ OD|od|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ length|length|NN|_ of|of|IN|_ time|time|NN|_ .|.|.|_
Carol|Carol|NNP|_ ,|,|,|_ A|A|NNP|_ ,|,|,|_ Gross|Gross|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp|exp|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp|exp|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp|exp|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ ACSH|ACSH|NNP|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp|exp|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Trans|Trans|NNP|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Trans|Trans|NNP|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Trans|Trans|NNP|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Trans|Trans|NNP|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Trans|Trans|NNP|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat1|stat1|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat1|stat1|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat1|stat1|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat1|stat1|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ --|--|:|_ nofw|nofw|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Probabilistic|Probabilistic|NNP|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat1|stat1|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol/vol|vol/vol|NN|_ -RRB-|-rrb-|-RRB-|_ unbuffered|unbuffered|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ EP|ep|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ traces|trace|NNS|_ of|of|IN|_ hydrolysate|hydrolysate|NN|_ ,|,|,|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ twice|twice|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ GMM|gmm|NN|_ plus|plus|CC|_ 0.125|0.125|CD|_ volume|volume|NN|_ of|of|IN|_ EP|ep|NN|_ ,|,|,|_ repelleted|repellete|VBN|_ ,|,|,|_ then|then|RB|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Robert|Robert|NNP|_ ,|,|,|_ C|C|NNP|_ ,|,|,|_ Landick|Landick|NNP|_
Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ bioinformatics|bioinformatic|NNS|_ department|department|NN|_ did|do|VBD|_ a|a|DT|_ preliminary|preliminary|JJ|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ high-throughput|high-throughput|JJ|_ sequencing|sequencing|NN|_ results|result|NNS|_ which|which|WDT|_ included|include|VBD|_ the|the|DT|_ mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_ genome|genome|NN|_ database|database|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
We|we|PRP|_ then|then|RB|_ used|use|VBD|_ the|the|DT|_ mapped|map|VBN|_ files|file|NNS|_ to|to|TO|_ run|run|VB|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ estimates|estimate|VBZ|_ the|the|DT|_ relative|relative|JJ|_ abundance|abundance|NN|_ of|of|IN|_ the|the|DT|_ transcripts|transcript|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ Cuffdiff|Cuffdiff|NNP|_ to|to|TO|_ find|find|VB|_ significant|significant|JJ|_ changes|change|NNS|_ in|in|IN|_ transcript|transcript|NN|_ expression|expression|NN|_ when|when|WRB|_ comparing|compare|VBG|_ two|two|CD|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ ,|,|,|_ Williams|Williams|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|sample|NN|_ ...|...|:|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ following|follow|VBG|_ cell|cell|NN|_ lysis|lysis|NN|_ and|and|CC|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Andrade|Andrade|NNP|_ ,|,|,|_ Pobre|Pobre|NNP|_ et|et|FW|_ al.|al.|FW|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ precipitation|precipitation|NN|_ step|step|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ 300|300|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ MilliQ-water|MilliQ-water|NNP|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ RNA|rna|NN|_ samples|sample|NNS|_ was|be|VBD|_ evaluated|evaluate|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ treatment|treatment|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ remove|remove|VB|_ contaminant|contaminant|NN|_ DNA|dna|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ by|by|IN|_ the|the|DT|_ company|company|NN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ in|in|IN|_ Germany|Germany|NNP|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ from|from|IN|_ isolated|isolate|VBN|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ ~|~|NN|_ 0.03|0.03|CD|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ When|when|WRB|_ required|require|VBN|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ present|present|JJ|_ at|at|IN|_ the|the|DT|_ following|follow|VBG|_ concentrations|concentration|NNS|_ :|:|:|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ streptomycin/spectinomycin|streptomycin/spectinomycin|NNP|_ 20|20|CD|_ µg|µg|NN|_ ml-1|ml-1|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12-MG1693|k12-mg1693|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|Exponential|NNP|_ Phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ Wild-type|wild-type|JJ|_
Overnight|overnight|NN|_ cultures|culture|NNS|_ from|from|IN|_ isolated|isolate|VBN|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ ~|~|NN|_ 0.03|0.03|CD|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ When|when|WRB|_ required|require|VBN|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ present|present|JJ|_ at|at|IN|_ the|the|DT|_ following|follow|VBG|_ concentrations|concentration|NNS|_ :|:|:|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ streptomycin/spectinomycin|streptomycin/spectinomycin|NNP|_ 20|20|CD|_ µg|µg|NN|_ ml-1|ml-1|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ cells|cell|NNS|_
Cecilia|Cecilia|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ Arraiano|Arraiano|NNP|_
Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ bioinformatics|bioinformatic|NNS|_ department|department|NN|_ did|do|VBD|_ a|a|DT|_ preliminary|preliminary|JJ|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ high-throughput|high-throughput|JJ|_ sequencing|sequencing|NN|_ results|result|NNS|_ which|which|WDT|_ included|include|VBD|_ the|the|DT|_ mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_ genome|genome|NN|_ database|database|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
We|we|PRP|_ then|then|RB|_ used|use|VBD|_ the|the|DT|_ mapped|map|VBN|_ files|file|NNS|_ to|to|TO|_ run|run|VB|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ estimates|estimate|VBZ|_ the|the|DT|_ relative|relative|JJ|_ abundance|abundance|NN|_ of|of|IN|_ the|the|DT|_ transcripts|transcript|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ Cuffdiff|Cuffdiff|NNP|_ to|to|TO|_ find|find|VB|_ significant|significant|JJ|_ changes|change|NNS|_ in|in|IN|_ transcript|transcript|NN|_ expression|expression|NN|_ when|when|WRB|_ comparing|compare|VBG|_ two|two|CD|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ ,|,|,|_ Williams|Williams|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|sample|NN|_ ...|...|:|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ following|follow|VBG|_ cell|cell|NN|_ lysis|lysis|NN|_ and|and|CC|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Andrade|Andrade|NNP|_ ,|,|,|_ Pobre|Pobre|NNP|_ et|et|FW|_ al.|al.|FW|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ precipitation|precipitation|NN|_ step|step|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ 300|300|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ MilliQ-water|MilliQ-water|NNP|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ RNA|rna|NN|_ samples|sample|NNS|_ was|be|VBD|_ evaluated|evaluate|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ treatment|treatment|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ remove|remove|VB|_ contaminant|contaminant|NN|_ DNA|dna|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ by|by|IN|_ the|the|DT|_ company|company|NN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ in|in|IN|_ Germany|Germany|NNP|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ from|from|IN|_ isolated|isolate|VBN|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ ~|~|NN|_ 0.03|0.03|CD|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ When|when|WRB|_ required|require|VBN|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ present|present|JJ|_ at|at|IN|_ the|the|DT|_ following|follow|VBG|_ concentrations|concentration|NNS|_ :|:|:|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ streptomycin/spectinomycin|streptomycin/spectinomycin|NNP|_ 20|20|CD|_ µg|µg|NN|_ ml-1|ml-1|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12-MG1693|k12-mg1693|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|Exponential|NNP|_ Phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ RNase|rnase|NN|_ II|ii|CD|_ mutant|mutant|JJ|_
Overnight|overnight|NN|_ cultures|culture|NNS|_ from|from|IN|_ isolated|isolate|VBN|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ ~|~|NN|_ 0.03|0.03|CD|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ When|when|WRB|_ required|require|VBN|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ present|present|JJ|_ at|at|IN|_ the|the|DT|_ following|follow|VBG|_ concentrations|concentration|NNS|_ :|:|:|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ streptomycin/spectinomycin|streptomycin/spectinomycin|NNP|_ 20|20|CD|_ µg|µg|NN|_ ml-1|ml-1|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ cells|cell|NNS|_
Cecilia|Cecilia|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ Arraiano|Arraiano|NNP|_
Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ bioinformatics|bioinformatic|NNS|_ department|department|NN|_ did|do|VBD|_ a|a|DT|_ preliminary|preliminary|JJ|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ high-throughput|high-throughput|JJ|_ sequencing|sequencing|NN|_ results|result|NNS|_ which|which|WDT|_ included|include|VBD|_ the|the|DT|_ mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_ genome|genome|NN|_ database|database|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
We|we|PRP|_ then|then|RB|_ used|use|VBD|_ the|the|DT|_ mapped|map|VBN|_ files|file|NNS|_ to|to|TO|_ run|run|VB|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ estimates|estimate|VBZ|_ the|the|DT|_ relative|relative|JJ|_ abundance|abundance|NN|_ of|of|IN|_ the|the|DT|_ transcripts|transcript|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ Cuffdiff|Cuffdiff|NNP|_ to|to|TO|_ find|find|VB|_ significant|significant|JJ|_ changes|change|NNS|_ in|in|IN|_ transcript|transcript|NN|_ expression|expression|NN|_ when|when|WRB|_ comparing|compare|VBG|_ two|two|CD|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ ,|,|,|_ Williams|Williams|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|sample|NN|_ ...|...|:|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ following|follow|VBG|_ cell|cell|NN|_ lysis|lysis|NN|_ and|and|CC|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Andrade|Andrade|NNP|_ ,|,|,|_ Pobre|Pobre|NNP|_ et|et|FW|_ al.|al.|FW|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ precipitation|precipitation|NN|_ step|step|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ 300|300|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ MilliQ-water|MilliQ-water|NNP|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ RNA|rna|NN|_ samples|sample|NNS|_ was|be|VBD|_ evaluated|evaluate|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ treatment|treatment|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ remove|remove|VB|_ contaminant|contaminant|NN|_ DNA|dna|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ by|by|IN|_ the|the|DT|_ company|company|NN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ in|in|IN|_ Germany|Germany|NNP|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ from|from|IN|_ isolated|isolate|VBN|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ ~|~|NN|_ 0.03|0.03|CD|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ When|when|WRB|_ required|require|VBN|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ present|present|JJ|_ at|at|IN|_ the|the|DT|_ following|follow|VBG|_ concentrations|concentration|NNS|_ :|:|:|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ streptomycin/spectinomycin|streptomycin/spectinomycin|NNP|_ 20|20|CD|_ µg|µg|NN|_ ml-1|ml-1|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12-MG1693|k12-mg1693|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|Exponential|NNP|_ Phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ RNase|rnase|NN|_ R|r|NN|_ mutant|mutant|JJ|_
Overnight|overnight|NN|_ cultures|culture|NNS|_ from|from|IN|_ isolated|isolate|VBN|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ ~|~|NN|_ 0.03|0.03|CD|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ When|when|WRB|_ required|require|VBN|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ present|present|JJ|_ at|at|IN|_ the|the|DT|_ following|follow|VBG|_ concentrations|concentration|NNS|_ :|:|:|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ streptomycin/spectinomycin|streptomycin/spectinomycin|NNP|_ 20|20|CD|_ µg|µg|NN|_ ml-1|ml-1|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ cells|cell|NNS|_
Cecilia|Cecilia|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ Arraiano|Arraiano|NNP|_
Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ bioinformatics|bioinformatic|NNS|_ department|department|NN|_ did|do|VBD|_ a|a|DT|_ preliminary|preliminary|JJ|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ high-throughput|high-throughput|JJ|_ sequencing|sequencing|NN|_ results|result|NNS|_ which|which|WDT|_ included|include|VBD|_ the|the|DT|_ mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_ genome|genome|NN|_ database|database|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
We|we|PRP|_ then|then|RB|_ used|use|VBD|_ the|the|DT|_ mapped|map|VBN|_ files|file|NNS|_ to|to|TO|_ run|run|VB|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ estimates|estimate|VBZ|_ the|the|DT|_ relative|relative|JJ|_ abundance|abundance|NN|_ of|of|IN|_ the|the|DT|_ transcripts|transcript|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ Cuffdiff|Cuffdiff|NNP|_ to|to|TO|_ find|find|VB|_ significant|significant|JJ|_ changes|change|NNS|_ in|in|IN|_ transcript|transcript|NN|_ expression|expression|NN|_ when|when|WRB|_ comparing|compare|VBG|_ two|two|CD|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ ,|,|,|_ Williams|Williams|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|sample|NN|_ ...|...|:|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ following|follow|VBG|_ cell|cell|NN|_ lysis|lysis|NN|_ and|and|CC|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Andrade|Andrade|NNP|_ ,|,|,|_ Pobre|Pobre|NNP|_ et|et|FW|_ al.|al.|FW|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ precipitation|precipitation|NN|_ step|step|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ 300|300|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ MilliQ-water|MilliQ-water|NNP|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ RNA|rna|NN|_ samples|sample|NNS|_ was|be|VBD|_ evaluated|evaluate|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ treatment|treatment|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ remove|remove|VB|_ contaminant|contaminant|NN|_ DNA|dna|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ by|by|IN|_ the|the|DT|_ company|company|NN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ in|in|IN|_ Germany|Germany|NNP|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ from|from|IN|_ isolated|isolate|VBN|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ ~|~|NN|_ 0.03|0.03|CD|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ When|when|WRB|_ required|require|VBN|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ present|present|JJ|_ at|at|IN|_ the|the|DT|_ following|follow|VBG|_ concentrations|concentration|NNS|_ :|:|:|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ streptomycin/spectinomycin|streptomycin/spectinomycin|NNP|_ 20|20|CD|_ µg|µg|NN|_ ml-1|ml-1|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12-MG1693|k12-mg1693|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|Exponential|NNP|_ Phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ PNPase|pnpase|NN|_ mutant|mutant|JJ|_
Overnight|overnight|NN|_ cultures|culture|NNS|_ from|from|IN|_ isolated|isolate|VBN|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ ~|~|NN|_ 0.03|0.03|CD|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ When|when|WRB|_ required|require|VBN|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ present|present|JJ|_ at|at|IN|_ the|the|DT|_ following|follow|VBG|_ concentrations|concentration|NNS|_ :|:|:|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ streptomycin/spectinomycin|streptomycin/spectinomycin|NNP|_ 20|20|CD|_ µg|µg|NN|_ ml-1|ml-1|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ cells|cell|NNS|_
Cecilia|Cecilia|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ Arraiano|Arraiano|NNP|_
The|The|NNP|_ fastq|fastq|NN|_ files|file|NNS|_ of|of|IN|_ 36-bp|36-bp|JJ|_ sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ CASAVA|CASAVA|NNP|_ v1|v1|NN|_ .8|.8|CD|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ bulk|bulk|NN|_ RNET-seq|rnet-seq|NN|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ specific|specific|JJ|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ the|the|DT|_ Trimmomatic|trimmomatic|JJ|_ v0|v0|NN|_ .25|.25|CD|_ to|to|TO|_ obtain|obtain|VB|_ reads|read|VBZ|_ ≥|≥|SYM|_ 21-nt|21-nt|CD|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ .|.|.|_ The|the|DT|_ reads|read|VBZ|_ ≥|≥|SYM|_ 21-nt|21-nt|JJ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ strain|strain|NN|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 007779.1|007779.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Bowtie2|bowtie2|NN|_ v2|v2|NN|_ .1.0|.1.0|CD|_ with|with|IN|_ the|the|DT|_ default|default|NN|_ parameter|parameter|NN|_ .|.|.|_ A|a|DT|_ gene|gene|NN|_ annotation|annotation|NN|_ file|file|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ ftp|ftp|NN|GEN server|server|NN|_ of|of|IN|_ Ensembl|ensembl|NN|_ .|.|.|_
To|to|TO|_ analyze|analyze|VB|_ RNAP|rnap|NN|_ pausing|pause|VBG|_ on|on|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ chromosome|chromosome|NN|_ ,|,|,|_ we|we|PRP|_ counted|count|VBD|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ every|every|DT|_ genomic|genomic|JJ|_ nucleotide|nucleotide|NN|_ position|position|NN|_ using|use|VBG|_ the|the|DT|_ mpileup|mpileup|NN|_ command|command|NN|_ of|of|IN|_ SAM|SAM|NNP|_ tools|tool|NNS|_ v0|v0|VBP|_ .1.18|.1.18|CD|_ with|with|IN|_ --|--|:|_ A|a|DT|_ --|--|:|_ B|b|NN|_ parameters|parameter|NNS|_ .|.|.|_ Pausing|pause|VBG|_ sites|site|NNS|_ were|be|VBD|_ defined|define|VBN|_ P|p|NN|_ -LRB-|-lrb-|-LRB-|_ φ|φ|NN|_ ,|,|,|_ δ|δ|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ where|where|WRB|_ φ|φ|NN|_ is|be|VBZ|_ the|the|DT|_ minimal|minimal|JJ|_ fraction|fraction|NN|_ of|of|IN|_ having|have|VBG|_ 3|3|CD|_ '|'|''|_ RNA|rna|NN|_ ends|end|VBZ|_ in|in|IN|_ the|the|DT|_ mapped|map|VBN|_ reads|read|VBZ|_ and|and|CC|_ δ|δ|NN|_ is|be|VBZ|_ the|the|DT|_ minimal|minimal|JJ|_ read|read|NN|_ depth|depth|NN|_ for|for|IN|_ any|any|DT|_ genomic|genomic|JJ|_ position|position|NN|_ .|.|.|_ We|we|PRP|_ chose|choose|VBD|_ δ|δ|NN|_ to|to|TO|_ be|be|VB|_ 100|100|CD|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ 160|160|CD|_ for|for|IN|_ ΔgreAB|δgreab|NN|_ ,|,|,|_ which|which|WDT|_ normalized|normalize|VBD|_ these|these|DT|_ respective|respective|JJ|_ numbers|number|NNS|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ since|since|IN|_ there|there|EX|_ were|be|VBD|_ 1.6-fold|1.6-fold|RB|_ more|more|RBR|_ total|total|JJ|_ reads|read|VBZ|_ in|in|IN|_ the|the|DT|_ ΔgreAB|δgreab|NN|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ high|high|JJ|_ φ|φ|NN|_ parameter|parameter|NN|_ allowed|allow|VBD|_ us|we|PRP|_ to|to|TO|_ define|define|VB|_ a|a|DT|_ reliable|reliable|JJ|_ pause-inducing|pause-inducing|JJ|_ element|element|NN|_ for|for|IN|_ WT|WT|NNP|_ or|or|CC|_ ΔgreAB|δgreab|NN|_ cells|cell|NNS|_ .|.|.|_
The|the|DT|_ processed|process|VBN|_ data|datum|NNS|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ csv|csv|NN|_ -RRB-|-rrb-|-RRB-|_ includes|include|VBZ|_ information|information|NN|_ about|about|IN|_ genomic|genomic|JJ|_ position|position|NN|_ ,|,|,|_ reference/non-reference|reference/non-reference|NN|_ bases|basis|NNS|_ ,|,|,|_ read|read|VBD|_ count|count|NN|_ ,|,|,|_ the|the|DT|_ fraction|fraction|NN|_ of|of|IN|_ 3|3|CD|_ '|'|''|_ RNA|rna|NN|_ end|end|NN|_ ,|,|,|_ DNA|dna|NN|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ /|/|:|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ gene|gene|NN|_ name|name|NN|_ ,|,|,|_ and|and|CC|_ mapping/base|mapping/base|NN|_ qualities|quality|NNS|_ in|in|IN|_ transcriptional|transcriptional|JJ|_ pause|pause|NN|_ sites|site|NNS|_ that|that|WDT|_ are|be|VBP|_ defined|define|VBN|_ by|by|IN|_ the|the|DT|_ parameters|parameter|NNS|_ P|p|NN|_ -LRB-|-lrb-|-LRB-|_ 0.9,100|0.9,100|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ 200|200|CD|_ ml|ml|NN|_ eluate|eluate|NN|_ from|from|IN|_ the|the|DT|_ Ni-NTA|ni-nta|NN|_ agarose|agarose|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ pre-warmed|pre-warmed|JJ|_ PCI|pci|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 70|70|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ and|and|CC|_ DNA|dna|NN|_ were|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ isopropanol|isopropanol|NN|_ from|from|IN|_ the|the|DT|_ supernatant|supernatant|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ dissolved|dissolve|VBN|_ in|in|IN|_ 30|30|CD|_ ml|ml|NN|_ DNase|dnase|NN|_ I|i|CD|_ buffer|buffer|NN|_ with|with|IN|_ 5|5|CD|_ U|U|NNP|_ DNaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Takara|Takara|NNP|_ Bio|Bio|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 20|20|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ separated|separate|VBN|_ from|from|IN|_ the|the|DT|_ digested|digest|VBN|_ DNA|dna|NN|_ by|by|IN|_ the|the|DT|_ PCI|pci|NN|_ extraction|extraction|NN|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ dissolved|dissolve|VBN|_ in|in|IN|_ diethylpyrocarbonate-treated|diethylpyrocarbonate-treated|JJ|_ water|water|NN|_ and|and|CC|_ used|use|VBN|_ for|for|IN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ .|.|.|_
cDNA|cdna|NN|_ library|library|NN|_ of|of|IN|_ the|the|DT|_ nascent|nascent|JJ|_ RNA|rna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ according|accord|VBG|_ to|to|TO|_ Churchman|Churchman|NNP|_ and|and|CC|_ Weissman|Weissman|NNP|_ ,|,|,|_ Nature|Nature|NNP|_ 2011|2011|CD|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 21248844|21248844|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ ~|~|NN|_ 300|300|CD|_ ml|ml|NN|_ LB|lb|NN|MED broth|broth|NN|MED +25|+25|CD|_ mg/ml|mg/ml|NN|_ kanamycin|kanamycin|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.5|0.5|CD|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ of|of|IN|_ 150|150|CD|_ mg|mg|NN|_ -LRB-|-lrb-|-LRB-|_ wet|wet|JJ|_ weight|weight|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 6,500|6,500|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 4|4|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ aliquoted|aliquote|VBN|_ in|in|IN|_ three|three|CD|_ 1.5|1.5|CD|_ ml|ml|NN|_ tubes|tube|NNS|_ ,|,|,|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
W3110|w3110|NN|_ rpoC-6xHis|rpoc-6xhis|NN|_ :|:|:|_ :|:|:|_ kan|kan|FW|_ gal490|gal490|FW|_
Each|each|DT|_ tube|tube|NN|_ of|of|IN|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 650|650|CD|_ ml|ml|NN|_ TES|tes|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.5|7.5|CD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ TritonX|tritonx|NN|_ 100|100|CD|_ ,|,|,|_ 0.3|0.3|CD|_ mM|mm|NN|KWSUPP PMSF|pmsf|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ suspension|suspension|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 100|100|CD|_ kU|ku|NN|_ Ready-Lyse|Ready-Lyse|NNP|_ Lysozyme|Lysozyme|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 50|50|CD|_ µg|µg|NN|_ RNaseA|rnasea|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ allowing|allow|VBG|_ rapid|rapid|JJ|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_ To|to|TO|_ digest|digest|VB|_ the|the|DT|_ nucleoide|nucleoide|NN|_ ,|,|,|_ 62.5|62.5|CD|_ U|U|NNP|_ DNaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 250|250|CD|_ µg/ml|µg/ml|JJ|_ heparin|heparin|NN|_ at|at|IN|_ the|the|DT|_ final|final|JJ|_ concentrations|concentration|NNS|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ 74|74|CD|_ ml|ml|NN|_ DNaseI|dnasei|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP MnCl2|mncl2|NN|SUPP 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ mixture|mixture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ cell|cell|NN|_ debris|debris|NN|_ ,|,|,|_ the|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 20,000|20,000|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ and|and|CC|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ new|new|JJ|_ 1.5|1.5|CD|_ ml|ml|NN|_ tube|tube|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|JJ|_ including|include|VBG|_ RNAPs|rnap|NNS|_ that|that|WDT|_ form|form|VBP|_ ternary|ternary|JJ|_ complexes|complex|NNS|_ with|with|IN|_ RNA/DNA|rna/dna|NN|_ were|be|VBD|_ immobilized|immobilize|VBN|_ on|on|IN|_ ~|~|NN|_ 155|155|CD|_ µl|µl|NN|_ Ni-NTA|ni-nta|NN|_ agarose|agarose|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ pre-equilibrated|pre-equilibrated|JJ|_ with|with|IN|_ the|the|DT|_ binding|binding|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 5|5|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH7|ph7|NN|_ .9|.9|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ immobilized|immobilize|VBN|_ ternary|ternary|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ washed|wash|VBN|_ five|five|CD|_ times|time|NNS|_ with|with|IN|_ the|the|DT|_ wash|wash|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 1M|1m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 15|15|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ pH7|ph7|NN|_ .9|.9|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ nuclease|nuclease|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 40|40|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ,|,|,|_ 15|15|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.9|7.9|CD|_ ,|,|,|_ 0.3|0.3|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ transcript|transcript|NN|_ and|and|CC|_ DNA|dna|NN|_ unprotected|unprotected|JJ|_ by|by|IN|_ RNAP|rnap|NN|_ were|be|VBD|_ cleaved|cleave|VBN|_ by|by|IN|_ the|the|DT|_ additions|addition|NNS|_ of|of|IN|_ 0.4|0.4|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 0.7|0.7|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Takara|Takara|NNP|_ Bio|Bio|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ the|the|DT|_ immobilized|immobilize|VBN|_ complexes|complex|NNS|_ and|and|CC|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ The|the|DT|_ nuclease-treated|nuclease-treated|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ wash|wash|NN|_ buffer|buffer|NN|_ ,|,|,|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ MnCl2-free|mncl2-free|NN|_ nuclease|nuclease|NN|_ buffer|buffer|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ by|by|IN|_ increasing|increase|VBG|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ imidazole|imidazole|NN|_ to|to|TO|_ 100|100|CD|_ mM|mm|NN|KWSUPP followed|follow|VBN|_ by|by|IN|_ shaking|shake|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 30|30|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ RNase|rnase|NN|_ inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ W3110|w3110|NN|_ rpoC-6xHis|rpoc-6xhis|NN|_ :|:|:|_ :|:|:|_ kan|kan|FW|_ gal490|gal490|FW|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ nascent|nascent|JJ|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ RNA|rna|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ ~|~|NN|_ 300|300|CD|_ ml|ml|NN|_ LB|lb|NN|MED broth|broth|NN|MED +25|+25|CD|_ mg/ml|mg/ml|NN|_ kanamycin|kanamycin|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.5|0.5|CD|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ of|of|IN|_ 150|150|CD|_ mg|mg|NN|_ -LRB-|-lrb-|-LRB-|_ wet|wet|JJ|_ weight|weight|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 6,500|6,500|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 4|4|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ aliquoted|aliquote|VBN|_ in|in|IN|_ three|three|CD|_ 1.5|1.5|CD|_ ml|ml|NN|_ tubes|tube|NNS|_ ,|,|,|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
W3110|w3110|NN|_ rpoC-6xHis|rpoc-6xhis|NN|_ :|:|:|_ :|:|:|_ kan|kan|FW|_ gal490|gal490|FW|_
Each|each|DT|_ tube|tube|NN|_ of|of|IN|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 650|650|CD|_ ml|ml|NN|_ TES|tes|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.5|7.5|CD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ TritonX|tritonx|NN|_ 100|100|CD|_ ,|,|,|_ 0.3|0.3|CD|_ mM|mm|NN|KWSUPP PMSF|pmsf|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ suspension|suspension|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 100|100|CD|_ kU|ku|NN|_ Ready-Lyse|Ready-Lyse|NNP|_ Lysozyme|Lysozyme|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 50|50|CD|_ µg|µg|NN|_ RNaseA|rnasea|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ allowing|allow|VBG|_ rapid|rapid|JJ|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_ To|to|TO|_ digest|digest|VB|_ the|the|DT|_ nucleoide|nucleoide|NN|_ ,|,|,|_ 62.5|62.5|CD|_ U|U|NNP|_ DNaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 250|250|CD|_ µg/ml|µg/ml|JJ|_ heparin|heparin|NN|_ at|at|IN|_ the|the|DT|_ final|final|JJ|_ concentrations|concentration|NNS|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ 74|74|CD|_ ml|ml|NN|_ DNaseI|dnasei|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP MnCl2|mncl2|NN|SUPP 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ mixture|mixture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ cell|cell|NN|_ debris|debris|NN|_ ,|,|,|_ the|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 20,000|20,000|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ and|and|CC|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ new|new|JJ|_ 1.5|1.5|CD|_ ml|ml|NN|_ tube|tube|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|JJ|_ including|include|VBG|_ RNAPs|rnap|NNS|_ that|that|WDT|_ form|form|VBP|_ ternary|ternary|JJ|_ complexes|complex|NNS|_ with|with|IN|_ RNA/DNA|rna/dna|NN|_ were|be|VBD|_ immobilized|immobilize|VBN|_ on|on|IN|_ ~|~|NN|_ 155|155|CD|_ µl|µl|NN|_ Ni-NTA|ni-nta|NN|_ agarose|agarose|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ pre-equilibrated|pre-equilibrated|JJ|_ with|with|IN|_ the|the|DT|_ binding|binding|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 5|5|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH7|ph7|NN|_ .9|.9|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ immobilized|immobilize|VBN|_ ternary|ternary|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ washed|wash|VBN|_ five|five|CD|_ times|time|NNS|_ with|with|IN|_ the|the|DT|_ wash|wash|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 1M|1m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 15|15|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ pH7|ph7|NN|_ .9|.9|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ nuclease|nuclease|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 40|40|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ,|,|,|_ 15|15|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.9|7.9|CD|_ ,|,|,|_ 0.3|0.3|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ transcript|transcript|NN|_ and|and|CC|_ DNA|dna|NN|_ unprotected|unprotected|JJ|_ by|by|IN|_ RNAP|rnap|NN|_ were|be|VBD|_ cleaved|cleave|VBN|_ by|by|IN|_ the|the|DT|_ additions|addition|NNS|_ of|of|IN|_ 0.4|0.4|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 0.7|0.7|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Takara|Takara|NNP|_ Bio|Bio|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ the|the|DT|_ immobilized|immobilize|VBN|_ complexes|complex|NNS|_ and|and|CC|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ The|the|DT|_ nuclease-treated|nuclease-treated|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ wash|wash|NN|_ buffer|buffer|NN|_ ,|,|,|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ MnCl2-free|mncl2-free|NN|_ nuclease|nuclease|NN|_ buffer|buffer|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ by|by|IN|_ increasing|increase|VBG|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ imidazole|imidazole|NN|_ to|to|TO|_ 100|100|CD|_ mM|mm|NN|KWSUPP followed|follow|VBN|_ by|by|IN|_ shaking|shake|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 30|30|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ RNase|rnase|NN|_ inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Masahiko|Masahiko|NNP|_ ,|,|,|_ ,|,|,|_ Imashimizu|Imashimizu|NNP|_
The|The|NNP|_ fastq|fastq|NN|_ files|file|NNS|_ of|of|IN|_ 36-bp|36-bp|JJ|_ sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ CASAVA|CASAVA|NNP|_ v1|v1|NN|_ .8|.8|CD|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ bulk|bulk|NN|_ RNET-seq|rnet-seq|NN|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ specific|specific|JJ|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ the|the|DT|_ Trimmomatic|trimmomatic|JJ|_ v0|v0|NN|_ .25|.25|CD|_ to|to|TO|_ obtain|obtain|VB|_ reads|read|VBZ|_ ≥|≥|SYM|_ 21-nt|21-nt|CD|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ .|.|.|_ The|the|DT|_ reads|read|VBZ|_ ≥|≥|SYM|_ 21-nt|21-nt|JJ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ strain|strain|NN|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 007779.1|007779.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Bowtie2|bowtie2|NN|_ v2|v2|NN|_ .1.0|.1.0|CD|_ with|with|IN|_ the|the|DT|_ default|default|NN|_ parameter|parameter|NN|_ .|.|.|_ A|a|DT|_ gene|gene|NN|_ annotation|annotation|NN|_ file|file|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ ftp|ftp|NN|GEN server|server|NN|_ of|of|IN|_ Ensembl|ensembl|NN|_ .|.|.|_
To|to|TO|_ analyze|analyze|VB|_ RNAP|rnap|NN|_ pausing|pause|VBG|_ on|on|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ chromosome|chromosome|NN|_ ,|,|,|_ we|we|PRP|_ counted|count|VBD|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ every|every|DT|_ genomic|genomic|JJ|_ nucleotide|nucleotide|NN|_ position|position|NN|_ using|use|VBG|_ the|the|DT|_ mpileup|mpileup|NN|_ command|command|NN|_ of|of|IN|_ SAM|SAM|NNP|_ tools|tool|NNS|_ v0|v0|VBP|_ .1.18|.1.18|CD|_ with|with|IN|_ --|--|:|_ A|a|DT|_ --|--|:|_ B|b|NN|_ parameters|parameter|NNS|_ .|.|.|_ Pausing|pause|VBG|_ sites|site|NNS|_ were|be|VBD|_ defined|define|VBN|_ P|p|NN|_ -LRB-|-lrb-|-LRB-|_ φ|φ|NN|_ ,|,|,|_ δ|δ|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ where|where|WRB|_ φ|φ|NN|_ is|be|VBZ|_ the|the|DT|_ minimal|minimal|JJ|_ fraction|fraction|NN|_ of|of|IN|_ having|have|VBG|_ 3|3|CD|_ '|'|''|_ RNA|rna|NN|_ ends|end|VBZ|_ in|in|IN|_ the|the|DT|_ mapped|map|VBN|_ reads|read|VBZ|_ and|and|CC|_ δ|δ|NN|_ is|be|VBZ|_ the|the|DT|_ minimal|minimal|JJ|_ read|read|NN|_ depth|depth|NN|_ for|for|IN|_ any|any|DT|_ genomic|genomic|JJ|_ position|position|NN|_ .|.|.|_ We|we|PRP|_ chose|choose|VBD|_ δ|δ|NN|_ to|to|TO|_ be|be|VB|_ 100|100|CD|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ 160|160|CD|_ for|for|IN|_ ΔgreAB|δgreab|NN|_ ,|,|,|_ which|which|WDT|_ normalized|normalize|VBD|_ these|these|DT|_ respective|respective|JJ|_ numbers|number|NNS|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ since|since|IN|_ there|there|EX|_ were|be|VBD|_ 1.6-fold|1.6-fold|RB|_ more|more|RBR|_ total|total|JJ|_ reads|read|VBZ|_ in|in|IN|_ the|the|DT|_ ΔgreAB|δgreab|NN|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ high|high|JJ|_ φ|φ|NN|_ parameter|parameter|NN|_ allowed|allow|VBD|_ us|we|PRP|_ to|to|TO|_ define|define|VB|_ a|a|DT|_ reliable|reliable|JJ|_ pause-inducing|pause-inducing|JJ|_ element|element|NN|_ for|for|IN|_ WT|WT|NNP|_ or|or|CC|_ ΔgreAB|δgreab|NN|_ cells|cell|NNS|_ .|.|.|_
The|the|DT|_ processed|process|VBN|_ data|datum|NNS|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ csv|csv|NN|_ -RRB-|-rrb-|-RRB-|_ includes|include|VBZ|_ information|information|NN|_ about|about|IN|_ genomic|genomic|JJ|_ position|position|NN|_ ,|,|,|_ reference/non-reference|reference/non-reference|NN|_ bases|basis|NNS|_ ,|,|,|_ read|read|VBD|_ count|count|NN|_ ,|,|,|_ the|the|DT|_ fraction|fraction|NN|_ of|of|IN|_ 3|3|CD|_ '|'|''|_ RNA|rna|NN|_ end|end|NN|_ ,|,|,|_ DNA|dna|NN|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ /|/|:|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ gene|gene|NN|_ name|name|NN|_ ,|,|,|_ and|and|CC|_ mapping/base|mapping/base|NN|_ qualities|quality|NNS|_ in|in|IN|_ transcriptional|transcriptional|JJ|_ pause|pause|NN|_ sites|site|NNS|_ that|that|WDT|_ are|be|VBP|_ defined|define|VBN|_ by|by|IN|_ the|the|DT|_ parameters|parameter|NNS|_ P|p|NN|_ -LRB-|-lrb-|-LRB-|_ 0.9|0.9|CD|_ ,|,|,|_ 160|160|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ 200|200|CD|_ ml|ml|NN|_ eluate|eluate|NN|_ from|from|IN|_ the|the|DT|_ Ni-NTA|ni-nta|NN|_ agarose|agarose|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ pre-warmed|pre-warmed|JJ|_ PCI|pci|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 70|70|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ and|and|CC|_ DNA|dna|NN|_ were|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ isopropanol|isopropanol|NN|_ from|from|IN|_ the|the|DT|_ supernatant|supernatant|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ dissolved|dissolve|VBN|_ in|in|IN|_ 30|30|CD|_ ml|ml|NN|_ DNase|dnase|NN|_ I|i|CD|_ buffer|buffer|NN|_ with|with|IN|_ 5|5|CD|_ U|U|NNP|_ DNaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Takara|Takara|NNP|_ Bio|Bio|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 20|20|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ separated|separate|VBN|_ from|from|IN|_ the|the|DT|_ digested|digest|VBN|_ DNA|dna|NN|_ by|by|IN|_ the|the|DT|_ PCI|pci|NN|_ extraction|extraction|NN|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ dissolved|dissolve|VBN|_ in|in|IN|_ diethylpyrocarbonate-treated|diethylpyrocarbonate-treated|JJ|_ water|water|NN|_ and|and|CC|_ used|use|VBN|_ for|for|IN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ .|.|.|_
cDNA|cdna|NN|_ library|library|NN|_ of|of|IN|_ the|the|DT|_ nascent|nascent|JJ|_ RNA|rna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ according|accord|VBG|_ to|to|TO|_ Churchman|Churchman|NNP|_ and|and|CC|_ Weissman|Weissman|NNP|_ ,|,|,|_ Nature|Nature|NNP|_ 2011|2011|CD|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 21248844|21248844|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ ~|~|NN|_ 300|300|CD|_ ml|ml|NN|_ LB|lb|NN|MED broth|broth|NN|MED +25|+25|CD|_ mg/ml|mg/ml|NN|_ kanamycin|kanamycin|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.5|0.5|CD|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ of|of|IN|_ 150|150|CD|_ mg|mg|NN|_ -LRB-|-lrb-|-LRB-|_ wet|wet|JJ|_ weight|weight|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 6,500|6,500|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 4|4|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ aliquoted|aliquote|VBN|_ in|in|IN|_ three|three|CD|_ 1.5|1.5|CD|_ ml|ml|NN|_ tubes|tube|NNS|_ ,|,|,|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
W3110|w3110|NN|_ rpoC-6xHis|rpoc-6xhis|NN|_ :|:|:|_ :|:|:|_ kan|kan|NN|_ greA|grea|NN|GEN :|:|:|_ :|:|:|_ tet|tet|NN|_ ,|,|,|_ greB|greb|NN|GEN :|:|:|_ :|:|:|_ amp|amp|NN|_
Each|each|DT|_ tube|tube|NN|_ of|of|IN|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 650|650|CD|_ ml|ml|NN|_ TES|tes|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.5|7.5|CD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ TritonX|tritonx|NN|_ 100|100|CD|_ ,|,|,|_ 0.3|0.3|CD|_ mM|mm|NN|KWSUPP PMSF|pmsf|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ suspension|suspension|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 100|100|CD|_ kU|ku|NN|_ Ready-Lyse|Ready-Lyse|NNP|_ Lysozyme|Lysozyme|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 50|50|CD|_ µg|µg|NN|_ RNaseA|rnasea|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ allowing|allow|VBG|_ rapid|rapid|JJ|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_ To|to|TO|_ digest|digest|VB|_ the|the|DT|_ nucleoide|nucleoide|NN|_ ,|,|,|_ 62.5|62.5|CD|_ U|U|NNP|_ DNaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 250|250|CD|_ µg/ml|µg/ml|JJ|_ heparin|heparin|NN|_ at|at|IN|_ the|the|DT|_ final|final|JJ|_ concentrations|concentration|NNS|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ 74|74|CD|_ ml|ml|NN|_ DNaseI|dnasei|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP MnCl2|mncl2|NN|SUPP 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ mixture|mixture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ cell|cell|NN|_ debris|debris|NN|_ ,|,|,|_ the|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 20,000|20,000|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ and|and|CC|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ new|new|JJ|_ 1.5|1.5|CD|_ ml|ml|NN|_ tube|tube|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|JJ|_ including|include|VBG|_ RNAPs|rnap|NNS|_ that|that|WDT|_ form|form|VBP|_ ternary|ternary|JJ|_ complexes|complex|NNS|_ with|with|IN|_ RNA/DNA|rna/dna|NN|_ were|be|VBD|_ immobilized|immobilize|VBN|_ on|on|IN|_ ~|~|NN|_ 155|155|CD|_ µl|µl|NN|_ Ni-NTA|ni-nta|NN|_ agarose|agarose|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ pre-equilibrated|pre-equilibrated|JJ|_ with|with|IN|_ the|the|DT|_ binding|binding|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 5|5|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH7|ph7|NN|_ .9|.9|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ immobilized|immobilize|VBN|_ ternary|ternary|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ washed|wash|VBN|_ five|five|CD|_ times|time|NNS|_ with|with|IN|_ the|the|DT|_ wash|wash|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 1M|1m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 15|15|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ pH7|ph7|NN|_ .9|.9|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ nuclease|nuclease|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 40|40|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ,|,|,|_ 15|15|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.9|7.9|CD|_ ,|,|,|_ 0.3|0.3|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ transcript|transcript|NN|_ and|and|CC|_ DNA|dna|NN|_ unprotected|unprotected|JJ|_ by|by|IN|_ RNAP|rnap|NN|_ were|be|VBD|_ cleaved|cleave|VBN|_ by|by|IN|_ the|the|DT|_ additions|addition|NNS|_ of|of|IN|_ 0.4|0.4|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 0.7|0.7|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Takara|Takara|NNP|_ Bio|Bio|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ the|the|DT|_ immobilized|immobilize|VBN|_ complexes|complex|NNS|_ and|and|CC|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ The|the|DT|_ nuclease-treated|nuclease-treated|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ wash|wash|NN|_ buffer|buffer|NN|_ ,|,|,|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ MnCl2-free|mncl2-free|NN|_ nuclease|nuclease|NN|_ buffer|buffer|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ by|by|IN|_ increasing|increase|VBG|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ imidazole|imidazole|NN|_ to|to|TO|_ 100|100|CD|_ mM|mm|NN|KWSUPP followed|follow|VBN|_ by|by|IN|_ shaking|shake|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 30|30|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ RNase|rnase|NN|_ inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ W3110|w3110|NN|_ rpoC-6xHis|rpoc-6xhis|NN|_ :|:|:|_ :|:|:|_ kan|kan|NN|_ greA|grea|NN|GEN :|:|:|_ :|:|:|_ tet|tet|NN|_ ,|,|,|_ greB|greb|NN|GEN :|:|:|_ :|:|:|_ amp|amp|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ nascent|nascent|JJ|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ RNA|rna|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ ~|~|NN|_ 300|300|CD|_ ml|ml|NN|_ LB|lb|NN|MED broth|broth|NN|MED +25|+25|CD|_ mg/ml|mg/ml|NN|_ kanamycin|kanamycin|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.5|0.5|CD|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ of|of|IN|_ 150|150|CD|_ mg|mg|NN|_ -LRB-|-lrb-|-LRB-|_ wet|wet|JJ|_ weight|weight|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 6,500|6,500|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 4|4|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ aliquoted|aliquote|VBN|_ in|in|IN|_ three|three|CD|_ 1.5|1.5|CD|_ ml|ml|NN|_ tubes|tube|NNS|_ ,|,|,|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
W3110|w3110|NN|_ rpoC-6xHis|rpoc-6xhis|NN|_ :|:|:|_ :|:|:|_ kan|kan|NN|_ greA|grea|NN|GEN :|:|:|_ :|:|:|_ tet|tet|NN|_ ,|,|,|_ greB|greb|NN|GEN :|:|:|_ :|:|:|_ amp|amp|NN|_
Each|each|DT|_ tube|tube|NN|_ of|of|IN|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 650|650|CD|_ ml|ml|NN|_ TES|tes|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.5|7.5|CD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ TritonX|tritonx|NN|_ 100|100|CD|_ ,|,|,|_ 0.3|0.3|CD|_ mM|mm|NN|KWSUPP PMSF|pmsf|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ suspension|suspension|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 100|100|CD|_ kU|ku|NN|_ Ready-Lyse|Ready-Lyse|NNP|_ Lysozyme|Lysozyme|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 50|50|CD|_ µg|µg|NN|_ RNaseA|rnasea|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ allowing|allow|VBG|_ rapid|rapid|JJ|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_ To|to|TO|_ digest|digest|VB|_ the|the|DT|_ nucleoide|nucleoide|NN|_ ,|,|,|_ 62.5|62.5|CD|_ U|U|NNP|_ DNaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 250|250|CD|_ µg/ml|µg/ml|JJ|_ heparin|heparin|NN|_ at|at|IN|_ the|the|DT|_ final|final|JJ|_ concentrations|concentration|NNS|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ 74|74|CD|_ ml|ml|NN|_ DNaseI|dnasei|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP MnCl2|mncl2|NN|SUPP 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ mixture|mixture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ cell|cell|NN|_ debris|debris|NN|_ ,|,|,|_ the|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 20,000|20,000|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ and|and|CC|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ new|new|JJ|_ 1.5|1.5|CD|_ ml|ml|NN|_ tube|tube|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|JJ|_ including|include|VBG|_ RNAPs|rnap|NNS|_ that|that|WDT|_ form|form|VBP|_ ternary|ternary|JJ|_ complexes|complex|NNS|_ with|with|IN|_ RNA/DNA|rna/dna|NN|_ were|be|VBD|_ immobilized|immobilize|VBN|_ on|on|IN|_ ~|~|NN|_ 155|155|CD|_ µl|µl|NN|_ Ni-NTA|ni-nta|NN|_ agarose|agarose|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ pre-equilibrated|pre-equilibrated|JJ|_ with|with|IN|_ the|the|DT|_ binding|binding|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 5|5|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH7|ph7|NN|_ .9|.9|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ immobilized|immobilize|VBN|_ ternary|ternary|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ washed|wash|VBN|_ five|five|CD|_ times|time|NNS|_ with|with|IN|_ the|the|DT|_ wash|wash|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 1M|1m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 15|15|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ pH7|ph7|NN|_ .9|.9|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ nuclease|nuclease|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 40|40|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ,|,|,|_ 15|15|CD|_ mM|mm|NN|KWSUPP imidazole|imidazole|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.9|7.9|CD|_ ,|,|,|_ 0.3|0.3|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ 5|5|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP 2-mercaptoethanol|2-mercaptoethanol|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ transcript|transcript|NN|_ and|and|CC|_ DNA|dna|NN|_ unprotected|unprotected|JJ|_ by|by|IN|_ RNAP|rnap|NN|_ were|be|VBD|_ cleaved|cleave|VBN|_ by|by|IN|_ the|the|DT|_ additions|addition|NNS|_ of|of|IN|_ 0.4|0.4|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 0.7|0.7|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Takara|Takara|NNP|_ Bio|Bio|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ the|the|DT|_ immobilized|immobilize|VBN|_ complexes|complex|NNS|_ and|and|CC|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ The|the|DT|_ nuclease-treated|nuclease-treated|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ wash|wash|NN|_ buffer|buffer|NN|_ ,|,|,|_ twice|twice|RB|_ with|with|IN|_ the|the|DT|_ MnCl2-free|mncl2-free|NN|_ nuclease|nuclease|NN|_ buffer|buffer|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ by|by|IN|_ increasing|increase|VBG|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ imidazole|imidazole|NN|_ to|to|TO|_ 100|100|CD|_ mM|mm|NN|KWSUPP followed|follow|VBN|_ by|by|IN|_ shaking|shake|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 30|30|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ RNase|rnase|NN|_ inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Masahiko|Masahiko|NNP|_ ,|,|,|_ ,|,|,|_ Imashimizu|Imashimizu|NNP|_
Base|Base|NNP|_ calling|call|VBG|_ performed|perform|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ GA|GA|NNP|_ pipeline|pipeline|NN|_ 1.6|1.6|CD|_ .|.|.|_
The|the|DT|_ clean|clean|JJ|_ reads|read|VBZ|_ obtained|obtain|VBN|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ sequence|sequence|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ using|use|VBG|_ SOAP2|soap2|NN|_
The|the|DT|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ filtered|filtered|VBN|_ for|for|IN|_ removing|remove|VBG|_ dirty|dirty|JJ|_ raw|raw|JJ|_ reads|read|VBZ|_ which|which|WDT|_ contain|contain|VBP|_ adapters|adapter|NNS|_ ,|,|,|_ unknown|unknown|JJ|_ or|or|CC|_ low|low|JJ|_ quality|quality|NN|_ bases|basis|NNS|_ .|.|.|_
All|all|PDT|_ those|those|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ level|level|NN|_ by|by|IN|_ the|the|DT|_ RPKM|rpkm|NN|_ method|method|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ able|able|JJ|_ to|to|TO|_ eliminate|eliminate|VB|_ the|the|DT|_ influence|influence|NN|_ of|of|IN|_ different|different|JJ|_ gene|gene|NN|_ length|length|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ discrepancy|discrepancy|NN|_ on|on|IN|_ the|the|DT|_ calculation|calculation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ and|and|CC|_ thus|thus|RB|_ the|the|DT|_ calculated|calculate|VBN|_ gene|gene|NN|_ expression|expression|NN|_ level|level|NN|_ can|can|MD|GEN be|be|VB|_ directly|directly|RB|_ used|use|VBN|_ for|for|IN|_ comparing|compare|VBG|_ the|the|DT|_ difference|difference|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ among|among|IN|_ samples|sample|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM666v1|asm666v1|NN|_ ;|;|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655.2|002655.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ excel|excel|VB|_ spreadsheet|spreadsheet|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ of|of|IN|_ sample|sample|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ VBNC|vbnc|NN|_ cells|cell|NNS|_ and|and|CC|_ the|the|DT|_ exponential-phase|exponential-phase|NN|_ cells|cell|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ Ⅰ|ⅰ|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
10|10|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ sample|sample|NN|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ purification|purification|NN|_ for|for|IN|_ discarding|discard|VBG|_ rRNA|rrna|NN|_ via|via|IN|_ the|the|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ interrupted|interrupt|VBN|_ into|into|IN|_ short|short|JJ|_ fragments|fragment|NNS|_ using|use|VBG|_ divalent|divalent|JJ|_ cations|cation|NNS|_ under|under|IN|_ elevated|elevated|JJ|_ temperature|temperature|NN|_ and|and|CC|_ the|the|DT|_ short|short|JJ|_ fragments|fragment|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ a|a|DT|_ SuperScript|SuperScript|NNP|_ Double-Stranded|Double-Stranded|NNP|_ cDNA|cdna|NN|_ Synthesis|synthesis|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ These|these|DT|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ a|a|DT|_ QIAquick|qiaquick|NN|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ went|go|VBD|_ through|through|IN|_ end|end|NN|_ reparation|reparation|NN|_ ,|,|,|_ adding|add|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ligation|ligation|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ adaptors|adaptor|NNS|_ .|.|.|_ These|these|DT|_ products|product|NNS|_ were|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ and|and|CC|_ fragments|fragment|NNS|_ in|in|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ 200-250|200-250|CD|_ bp|bp|NN|_ were|be|VBD|_ selected|select|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ to|to|TO|_ construct|construct|VB|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_
The|the|DT|_ strain|strain|NN|_ was|be|VBD|_ stocked|stock|VBN|_ in|in|IN|_ tryptic|tryptic|JJ|_ soy|soy|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ TSB|tsb|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 25|25|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ ,|,|,|_ and|and|CC|_ was|be|VBD|_ activated|activate|VBN|_ by|by|IN|_ streaking|streak|VBG|_ onto|onto|IN|_ TSA|TSA|NNP|_ plate|plate|NN|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 24|24|CD|_ h.|h.|NN|_ And|and|CC|_ then|then|RB|_ ,|,|,|_ a|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ picked|pick|VBN|_ and|and|CC|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ TSB|TSB|NNP|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ This|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ TSB|tsb|NN|_ at|at|IN|_ a|a|DT|_ dilution|dilution|NN|_ of|of|IN|_ 1:100|1:100|CD|_ and|and|CC|_ grew|grow|VBD|_ to|to|TO|_ the|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD550|od550|NN|_ =|=|JJ|_ 0.93|0.93|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterium|bacterium|NN|_
In|in|IN|_ order|order|NN|_ to|to|TO|_ generate|generate|VB|_ the|the|DT|_ VBNC|vbnc|JJ|_ state|state|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ ,|,|,|_ 20|20|CD|_ mL|ml|NN|_ of|of|IN|_ the|the|DT|_ exponential-phase|exponential-phase|NN|_ cell|cell|NN|_ suspensions|suspension|NNS|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ mL|ml|NN|_ sterile|sterile|JJ|_ glass|glass|NN|_ tube|tube|NN|_ was|be|VBD|_ treated|treat|VBN|_ by|by|IN|_ HPCD|hpcd|NN|_ at|at|IN|_ 5|5|CD|_ MPa|mpa|NN|_ and|and|CC|_ 25|25|CD|_ ℃|℃|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ NCTC|nctc|NN|_ 12900|12900|CD|_
treatment|treatment|NN|_ :|:|:|_ None|none|NN|_
The|the|DT|_ strain|strain|NN|_ was|be|VBD|_ stocked|stock|VBN|_ in|in|IN|_ tryptic|tryptic|JJ|_ soy|soy|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ TSB|tsb|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 25|25|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ ,|,|,|_ and|and|CC|_ was|be|VBD|_ activated|activate|VBN|_ by|by|IN|_ streaking|streak|VBG|_ onto|onto|IN|_ TSA|TSA|NNP|_ plate|plate|NN|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 24|24|CD|_ h.|h.|NN|_ And|and|CC|_ then|then|RB|_ ,|,|,|_ a|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ picked|pick|VBN|_ and|and|CC|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ TSB|TSB|NNP|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ This|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ TSB|tsb|NN|_ at|at|IN|_ a|a|DT|_ dilution|dilution|NN|_ of|of|IN|_ 1:100|1:100|CD|_ and|and|CC|_ grew|grow|VBD|_ to|to|TO|_ the|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD550|od550|NN|_ =|=|JJ|_ 0.93|0.93|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterium|bacterium|NN|_
In|in|IN|_ order|order|NN|_ to|to|TO|_ generate|generate|VB|_ the|the|DT|_ VBNC|vbnc|JJ|_ state|state|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ ,|,|,|_ 20|20|CD|_ mL|ml|NN|_ of|of|IN|_ the|the|DT|_ exponential-phase|exponential-phase|NN|_ cell|cell|NN|_ suspensions|suspension|NNS|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ mL|ml|NN|_ sterile|sterile|JJ|_ glass|glass|NN|_ tube|tube|NN|_ was|be|VBD|_ treated|treat|VBN|_ by|by|IN|_ HPCD|hpcd|NN|_ at|at|IN|_ 5|5|CD|_ MPa|mpa|NN|_ and|and|CC|_ 25|25|CD|_ ℃|℃|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_ .|.|.|_
Feng|Feng|NNP|_ ,|,|,|_ ,|,|,|_ Zhao|Zhao|NNP|_
Base|Base|NNP|_ calling|call|VBG|_ performed|perform|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ GA|GA|NNP|_ pipeline|pipeline|NN|_ 1.6|1.6|CD|_ .|.|.|_
The|the|DT|_ clean|clean|JJ|_ reads|read|VBZ|_ obtained|obtain|VBN|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ sequence|sequence|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ using|use|VBG|_ SOAP2|soap2|NN|_
The|the|DT|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ filtered|filtered|VBN|_ for|for|IN|_ removing|remove|VBG|_ dirty|dirty|JJ|_ raw|raw|JJ|_ reads|read|VBZ|_ which|which|WDT|_ contain|contain|VBP|_ adapters|adapter|NNS|_ ,|,|,|_ unknown|unknown|JJ|_ or|or|CC|_ low|low|JJ|_ quality|quality|NN|_ bases|basis|NNS|_ .|.|.|_
All|all|PDT|_ those|those|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ level|level|NN|_ by|by|IN|_ the|the|DT|_ RPKM|rpkm|NN|_ method|method|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ able|able|JJ|_ to|to|TO|_ eliminate|eliminate|VB|_ the|the|DT|_ influence|influence|NN|_ of|of|IN|_ different|different|JJ|_ gene|gene|NN|_ length|length|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ discrepancy|discrepancy|NN|_ on|on|IN|_ the|the|DT|_ calculation|calculation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ and|and|CC|_ thus|thus|RB|_ the|the|DT|_ calculated|calculate|VBN|_ gene|gene|NN|_ expression|expression|NN|_ level|level|NN|_ can|can|MD|GEN be|be|VB|_ directly|directly|RB|_ used|use|VBN|_ for|for|IN|_ comparing|compare|VBG|_ the|the|DT|_ difference|difference|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ among|among|IN|_ samples|sample|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM666v1|asm666v1|NN|_ ;|;|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655.2|002655.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ excel|excel|VB|_ spreadsheet|spreadsheet|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ of|of|IN|_ sample|sample|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ VBNC|vbnc|NN|_ cells|cell|NNS|_ and|and|CC|_ the|the|DT|_ exponential-phase|exponential-phase|NN|_ cells|cell|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ Ⅰ|ⅰ|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
10|10|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ sample|sample|NN|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ purification|purification|NN|_ for|for|IN|_ discarding|discard|VBG|_ rRNA|rrna|NN|_ via|via|IN|_ the|the|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ interrupted|interrupt|VBN|_ into|into|IN|_ short|short|JJ|_ fragments|fragment|NNS|_ using|use|VBG|_ divalent|divalent|JJ|_ cations|cation|NNS|_ under|under|IN|_ elevated|elevated|JJ|_ temperature|temperature|NN|_ and|and|CC|_ the|the|DT|_ short|short|JJ|_ fragments|fragment|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ a|a|DT|_ SuperScript|SuperScript|NNP|_ Double-Stranded|Double-Stranded|NNP|_ cDNA|cdna|NN|_ Synthesis|synthesis|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ These|these|DT|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ a|a|DT|_ QIAquick|qiaquick|NN|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ went|go|VBD|_ through|through|IN|_ end|end|NN|_ reparation|reparation|NN|_ ,|,|,|_ adding|add|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ligation|ligation|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ adaptors|adaptor|NNS|_ .|.|.|_ These|these|DT|_ products|product|NNS|_ were|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ and|and|CC|_ fragments|fragment|NNS|_ in|in|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ 200-250|200-250|CD|_ bp|bp|NN|_ were|be|VBD|_ selected|select|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ to|to|TO|_ construct|construct|VB|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_
The|the|DT|_ strain|strain|NN|_ was|be|VBD|_ stocked|stock|VBN|_ in|in|IN|_ tryptic|tryptic|JJ|_ soy|soy|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ TSB|tsb|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 25|25|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ ,|,|,|_ and|and|CC|_ was|be|VBD|_ activated|activate|VBN|_ by|by|IN|_ streaking|streak|VBG|_ onto|onto|IN|_ TSA|TSA|NNP|_ plate|plate|NN|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 24|24|CD|_ h.|h.|NN|_ And|and|CC|_ then|then|RB|_ ,|,|,|_ a|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ picked|pick|VBN|_ and|and|CC|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ TSB|TSB|NNP|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ This|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ TSB|tsb|NN|_ at|at|IN|_ a|a|DT|_ dilution|dilution|NN|_ of|of|IN|_ 1:100|1:100|CD|_ and|and|CC|_ grew|grow|VBD|_ to|to|TO|_ the|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD550|od550|NN|_ =|=|JJ|_ 0.93|0.93|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterium|bacterium|NN|_
In|in|IN|_ order|order|NN|_ to|to|TO|_ generate|generate|VB|_ the|the|DT|_ VBNC|vbnc|JJ|_ state|state|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ ,|,|,|_ 20|20|CD|_ mL|ml|NN|_ of|of|IN|_ the|the|DT|_ exponential-phase|exponential-phase|NN|_ cell|cell|NN|_ suspensions|suspension|NNS|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ mL|ml|NN|_ sterile|sterile|JJ|_ glass|glass|NN|_ tube|tube|NN|_ was|be|VBD|_ treated|treat|VBN|_ by|by|IN|_ HPCD|hpcd|NN|_ at|at|IN|_ 5|5|CD|_ MPa|mpa|NN|_ and|and|CC|_ 25|25|CD|_ ℃|℃|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ NCTC|nctc|NN|_ 12900|12900|CD|_
treatment|treatment|NN|_ :|:|:|_ Treated|treat|VBN|_ by|by|IN|_ HPCD|hpcd|NN|_ at|at|IN|_ 5|5|CD|_ MPa|mpa|NN|_ and|and|CC|_ 25|25|CD|_ ℃|℃|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
The|the|DT|_ strain|strain|NN|_ was|be|VBD|_ stocked|stock|VBN|_ in|in|IN|_ tryptic|tryptic|JJ|_ soy|soy|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ TSB|tsb|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 25|25|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ ,|,|,|_ and|and|CC|_ was|be|VBD|_ activated|activate|VBN|_ by|by|IN|_ streaking|streak|VBG|_ onto|onto|IN|_ TSA|TSA|NNP|_ plate|plate|NN|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 24|24|CD|_ h.|h.|NN|_ And|and|CC|_ then|then|RB|_ ,|,|,|_ a|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ picked|pick|VBN|_ and|and|CC|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ TSB|TSB|NNP|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ This|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ TSB|tsb|NN|_ at|at|IN|_ a|a|DT|_ dilution|dilution|NN|_ of|of|IN|_ 1:100|1:100|CD|_ and|and|CC|_ grew|grow|VBD|_ to|to|TO|_ the|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD550|od550|NN|_ =|=|JJ|_ 0.93|0.93|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacterium|bacterium|NN|_
In|in|IN|_ order|order|NN|_ to|to|TO|_ generate|generate|VB|_ the|the|DT|_ VBNC|vbnc|JJ|_ state|state|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ ,|,|,|_ 20|20|CD|_ mL|ml|NN|_ of|of|IN|_ the|the|DT|_ exponential-phase|exponential-phase|NN|_ cell|cell|NN|_ suspensions|suspension|NNS|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ mL|ml|NN|_ sterile|sterile|JJ|_ glass|glass|NN|_ tube|tube|NN|_ was|be|VBD|_ treated|treat|VBN|_ by|by|IN|_ HPCD|hpcd|NN|_ at|at|IN|_ 5|5|CD|_ MPa|mpa|NN|_ and|and|CC|_ 25|25|CD|_ ℃|℃|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_ .|.|.|_
Feng|Feng|NNP|_ ,|,|,|_ ,|,|,|_ Zhao|Zhao|NNP|_
Quality|Quality|NNP|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.2.1|1.2.1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 0.12.9|0.12.9|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 3|3|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Read|Read|NNP|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ the|the|DT|_ middle|middle|NN|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ the|the|DT|_ read|read|NN|_ count|count|NN|_ was|be|VBD|_ assigned|assign|VBN|_ to|to|TO|_ the|the|DT|_ nucleotide|nucleotide|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ see|see|VB|_ -LCB-|-lcb-|-LRB-|_ Kertesz|Kertesz|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RCB-|-rcb-|-RRB-|_ for|for|IN|_ details|detail|NNS|_
Read|Read|NNP|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ for|for|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ version|version|NN|_ U00096|u00096|NN|_ .2|.2|NN|_ ,|,|,|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Column|Column|NNP|_ 1|1|CD|_ names|name|NNS|_ the|the|DT|_ nucleotide|nucleotide|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ column|column|NN|_ 2|2|CD|_ gives|give|VBZ|_ counts|count|NNS|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ strand|strand|NN|_ ,|,|,|_ column|column|NN|_ 3|3|CD|_ for|for|IN|_ the|the|DT|_ reverse|reverse|JJ|_ strand|strand|NN|_ ,|,|,|_ columns|column|NNS|_ are|be|VBP|_ tab|tab|NN|_ separated|separated|JJ|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ enriched|enrich|VBN|_ in|in|IN|_ mRNA|mrna|NN|_ ,|,|,|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|genejet|NN|_ ™|™|NN|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ with|with|IN|_ two|two|CD|_ cycle|cycle|NN|_ of|of|IN|_ MICROBExpress|microbexpress|NN|_ ™|™|CD|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ probe|probe|VB|_ the|the|DT|_ RNA|rna|NN|_ structure|structure|NN|_ two|two|CD|_ µg|µg|NN|_ of|of|IN|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 45|45|CD|_ µl|µl|NN|_ of|of|IN|_ DEPC|depc|NN|_ water|water|NN|_ and|and|CC|_ denatured|denature|VBN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ ,|,|,|_ refolded|refold|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ 10x|10x|CD|_ RNA-structure|rna-structure|NN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 7.0|7.0|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ ,|,|,|_ 1|1|CD|_ M|m|NN|_ KCl|kcl|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ either|either|CC|_ 0.05|0.05|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ 2|2|CD|_ µg|µg|NN|_ RNase|rnase|NN|_ A|a|NN|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ stopped|stop|VBN|_ by|by|IN|_ extracting|extract|VBG|_ the|the|DT|_ RNA|rna|NN|_ with|with|IN|_ phenol-chlorophorm|phenol-chlorophorm|NN|_ .|.|.|_ The|the|DT|_ RNase|rnase|NN|_ A/T1-digested|a/t1-digested|JJ|_ sample|sample|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ with|with|IN|_ T4|t4|NN|_ PNK|pnk|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ purified|purify|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Both|both|CC|_ the|the|DT|_ V1|v1|NN|_ and|and|CC|_ A/T1|a/t1|NN|_ digested|digest|VBD|_ samples|sample|NNS|_ were|be|VBD|_ randomly|randomly|RB|_ fragmented|fragmented|JJ|_ in|in|IN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 9.2|9.2|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 12|12|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ .|.|.|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Alexander|Alexander|NNP|_ ,|,|,|_ ,|,|,|_ Bartholomaeus|Bartholomaeus|NNP|_
Quality|Quality|NNP|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.2.1|1.2.1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 0.12.9|0.12.9|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 3|3|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Read|Read|NNP|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ the|the|DT|_ middle|middle|NN|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ the|the|DT|_ read|read|NN|_ count|count|NN|_ was|be|VBD|_ assigned|assign|VBN|_ to|to|TO|_ the|the|DT|_ nucleotide|nucleotide|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ see|see|VB|_ -LCB-|-lcb-|-LRB-|_ Kertesz|Kertesz|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RCB-|-rcb-|-RRB-|_ for|for|IN|_ details|detail|NNS|_
Read|Read|NNP|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ for|for|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ version|version|NN|_ U00096|u00096|NN|_ .2|.2|NN|_ ,|,|,|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Column|Column|NNP|_ 1|1|CD|_ names|name|NNS|_ the|the|DT|_ nucleotide|nucleotide|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ column|column|NN|_ 2|2|CD|_ gives|give|VBZ|_ counts|count|NNS|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ strand|strand|NN|_ ,|,|,|_ column|column|NN|_ 3|3|CD|_ for|for|IN|_ the|the|DT|_ reverse|reverse|JJ|_ strand|strand|NN|_ ,|,|,|_ columns|column|NNS|_ are|be|VBP|_ tab|tab|NN|_ separated|separated|JJ|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ enriched|enrich|VBN|_ in|in|IN|_ mRNA|mrna|NN|_ ,|,|,|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|genejet|NN|_ ™|™|NN|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ with|with|IN|_ two|two|CD|_ cycle|cycle|NN|_ of|of|IN|_ MICROBExpress|microbexpress|NN|_ ™|™|CD|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ probe|probe|VB|_ the|the|DT|_ RNA|rna|NN|_ structure|structure|NN|_ two|two|CD|_ µg|µg|NN|_ of|of|IN|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 45|45|CD|_ µl|µl|NN|_ of|of|IN|_ DEPC|depc|NN|_ water|water|NN|_ and|and|CC|_ denatured|denature|VBN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ ,|,|,|_ refolded|refold|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ 10x|10x|CD|_ RNA-structure|rna-structure|NN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 7.0|7.0|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ ,|,|,|_ 1|1|CD|_ M|m|NN|_ KCl|kcl|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ either|either|CC|_ 0.05|0.05|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ 2|2|CD|_ µg|µg|NN|_ RNase|rnase|NN|_ A|a|NN|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ stopped|stop|VBN|_ by|by|IN|_ extracting|extract|VBG|_ the|the|DT|_ RNA|rna|NN|_ with|with|IN|_ phenol-chlorophorm|phenol-chlorophorm|NN|_ .|.|.|_ The|the|DT|_ RNase|rnase|NN|_ A/T1-digested|a/t1-digested|JJ|_ sample|sample|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ with|with|IN|_ T4|t4|NN|_ PNK|pnk|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ purified|purify|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Both|both|CC|_ the|the|DT|_ V1|v1|NN|_ and|and|CC|_ A/T1|a/t1|NN|_ digested|digest|VBD|_ samples|sample|NNS|_ were|be|VBD|_ randomly|randomly|RB|_ fragmented|fragmented|JJ|_ in|in|IN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 9.2|9.2|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 12|12|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ .|.|.|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ ribosome|ribosome|NN|_ protected|protect|VBD|_
E.|E.|NNP|_ coli|coli|NN|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Alexander|Alexander|NNP|_ ,|,|,|_ ,|,|,|_ Bartholomaeus|Bartholomaeus|NNP|_
Quality|Quality|NNP|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.2.1|1.2.1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 0.12.9|0.12.9|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 3|3|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Read|Read|NNP|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ the|the|DT|_ middle|middle|NN|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ the|the|DT|_ read|read|NN|_ count|count|NN|_ was|be|VBD|_ assigned|assign|VBN|_ to|to|TO|_ the|the|DT|_ nucleotide|nucleotide|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ see|see|VB|_ -LCB-|-lcb-|-LRB-|_ Kertesz|Kertesz|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RCB-|-rcb-|-RRB-|_ for|for|IN|_ details|detail|NNS|_
Read|Read|NNP|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ for|for|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ version|version|NN|_ U00096|u00096|NN|_ .2|.2|NN|_ ,|,|,|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Column|Column|NNP|_ 1|1|CD|_ names|name|NNS|_ the|the|DT|_ nucleotide|nucleotide|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ column|column|NN|_ 2|2|CD|_ gives|give|VBZ|_ counts|count|NNS|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ strand|strand|NN|_ ,|,|,|_ column|column|NN|_ 3|3|CD|_ for|for|IN|_ the|the|DT|_ reverse|reverse|JJ|_ strand|strand|NN|_ ,|,|,|_ columns|column|NNS|_ are|be|VBP|_ tab|tab|NN|_ separated|separated|JJ|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ enriched|enrich|VBN|_ in|in|IN|_ mRNA|mrna|NN|_ ,|,|,|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|genejet|NN|_ ™|™|NN|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ with|with|IN|_ two|two|CD|_ cycle|cycle|NN|_ of|of|IN|_ MICROBExpress|microbexpress|NN|_ ™|™|CD|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ probe|probe|VB|_ the|the|DT|_ RNA|rna|NN|_ structure|structure|NN|_ two|two|CD|_ µg|µg|NN|_ of|of|IN|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 45|45|CD|_ µl|µl|NN|_ of|of|IN|_ DEPC|depc|NN|_ water|water|NN|_ and|and|CC|_ denatured|denature|VBN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ ,|,|,|_ refolded|refold|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ 10x|10x|CD|_ RNA-structure|rna-structure|NN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 7.0|7.0|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ ,|,|,|_ 1|1|CD|_ M|m|NN|_ KCl|kcl|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ either|either|CC|_ 0.05|0.05|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ 2|2|CD|_ µg|µg|NN|_ RNase|rnase|NN|_ A|a|NN|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ stopped|stop|VBN|_ by|by|IN|_ extracting|extract|VBG|_ the|the|DT|_ RNA|rna|NN|_ with|with|IN|_ phenol-chlorophorm|phenol-chlorophorm|NN|_ .|.|.|_ The|the|DT|_ RNase|rnase|NN|_ A/T1-digested|a/t1-digested|JJ|_ sample|sample|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ with|with|IN|_ T4|t4|NN|_ PNK|pnk|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ purified|purify|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Both|both|CC|_ the|the|DT|_ V1|v1|NN|_ and|and|CC|_ A/T1|a/t1|NN|_ digested|digest|VBD|_ samples|sample|NNS|_ were|be|VBD|_ randomly|randomly|RB|_ fragmented|fragmented|JJ|_ in|in|IN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 9.2|9.2|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 12|12|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ .|.|.|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4101|mc4101|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Alexander|Alexander|NNP|_ ,|,|,|_ ,|,|,|_ Bartholomaeus|Bartholomaeus|NNP|_
Quality|Quality|NNP|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.2.1|1.2.1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 0.12.9|0.12.9|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 3|3|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Read|Read|NNP|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ the|the|DT|_ middle|middle|NN|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ the|the|DT|_ read|read|NN|_ count|count|NN|_ was|be|VBD|_ assigned|assign|VBN|_ to|to|TO|_ the|the|DT|_ nucleotide|nucleotide|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ see|see|VB|_ -LCB-|-lcb-|-LRB-|_ Kertesz|Kertesz|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RCB-|-rcb-|-RRB-|_ for|for|IN|_ details|detail|NNS|_
Read|Read|NNP|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ for|for|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ version|version|NN|_ U00096|u00096|NN|_ .2|.2|NN|_ ,|,|,|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Column|Column|NNP|_ 1|1|CD|_ names|name|NNS|_ the|the|DT|_ nucleotide|nucleotide|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ column|column|NN|_ 2|2|CD|_ gives|give|VBZ|_ counts|count|NNS|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ strand|strand|NN|_ ,|,|,|_ column|column|NN|_ 3|3|CD|_ for|for|IN|_ the|the|DT|_ reverse|reverse|JJ|_ strand|strand|NN|_ ,|,|,|_ columns|column|NNS|_ are|be|VBP|_ tab|tab|NN|_ separated|separated|JJ|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ enriched|enrich|VBN|_ in|in|IN|_ mRNA|mrna|NN|_ ,|,|,|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|genejet|NN|_ ™|™|NN|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ with|with|IN|_ two|two|CD|_ cycle|cycle|NN|_ of|of|IN|_ MICROBExpress|microbexpress|NN|_ ™|™|CD|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ probe|probe|VB|_ the|the|DT|_ RNA|rna|NN|_ structure|structure|NN|_ two|two|CD|_ µg|µg|NN|_ of|of|IN|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 45|45|CD|_ µl|µl|NN|_ of|of|IN|_ DEPC|depc|NN|_ water|water|NN|_ and|and|CC|_ denatured|denature|VBN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ ,|,|,|_ refolded|refold|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ 10x|10x|CD|_ RNA-structure|rna-structure|NN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 7.0|7.0|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ ,|,|,|_ 1|1|CD|_ M|m|NN|_ KCl|kcl|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ either|either|CC|_ 0.05|0.05|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ 2|2|CD|_ µg|µg|NN|_ RNase|rnase|NN|_ A|a|NN|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ stopped|stop|VBN|_ by|by|IN|_ extracting|extract|VBG|_ the|the|DT|_ RNA|rna|NN|_ with|with|IN|_ phenol-chlorophorm|phenol-chlorophorm|NN|_ .|.|.|_ The|the|DT|_ RNase|rnase|NN|_ A/T1-digested|a/t1-digested|JJ|_ sample|sample|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ with|with|IN|_ T4|t4|NN|_ PNK|pnk|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ purified|purify|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Both|both|CC|_ the|the|DT|_ V1|v1|NN|_ and|and|CC|_ A/T1|a/t1|NN|_ digested|digest|VBD|_ samples|sample|NNS|_ were|be|VBD|_ randomly|randomly|RB|_ fragmented|fragmented|JJ|_ in|in|IN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 9.2|9.2|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 12|12|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ .|.|.|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4102|mc4102|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ ribosome|ribosome|NN|_ protected|protect|VBD|_
E.|E.|NNP|_ coli|coli|NN|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Alexander|Alexander|NNP|_ ,|,|,|_ ,|,|,|_ Bartholomaeus|Bartholomaeus|NNP|_
Quality|Quality|NNP|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.2.1|1.2.1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 0.12.9|0.12.9|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 3|3|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Read|Read|NNP|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ the|the|DT|_ middle|middle|NN|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ the|the|DT|_ read|read|NN|_ count|count|NN|_ was|be|VBD|_ assigned|assign|VBN|_ to|to|TO|_ the|the|DT|_ nucleotide|nucleotide|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ see|see|VB|_ -LCB-|-lcb-|-LRB-|_ Kertesz|Kertesz|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RCB-|-rcb-|-RRB-|_ for|for|IN|_ details|detail|NNS|_
Read|Read|NNP|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ for|for|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ version|version|NN|_ U00096|u00096|NN|_ .2|.2|NN|_ ,|,|,|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Column|Column|NNP|_ 1|1|CD|_ names|name|NNS|_ the|the|DT|_ nucleotide|nucleotide|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ column|column|NN|_ 2|2|CD|_ gives|give|VBZ|_ counts|count|NNS|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ strand|strand|NN|_ ,|,|,|_ column|column|NN|_ 3|3|CD|_ for|for|IN|_ the|the|DT|_ reverse|reverse|JJ|_ strand|strand|NN|_ ,|,|,|_ columns|column|NNS|_ are|be|VBP|_ tab|tab|NN|_ separated|separated|JJ|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ enriched|enrich|VBN|_ in|in|IN|_ mRNA|mrna|NN|_ ,|,|,|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|genejet|NN|_ ™|™|NN|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ with|with|IN|_ two|two|CD|_ cycle|cycle|NN|_ of|of|IN|_ MICROBExpress|microbexpress|NN|_ ™|™|CD|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ probe|probe|VB|_ the|the|DT|_ RNA|rna|NN|_ structure|structure|NN|_ two|two|CD|_ µg|µg|NN|_ of|of|IN|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 45|45|CD|_ µl|µl|NN|_ of|of|IN|_ DEPC|depc|NN|_ water|water|NN|_ and|and|CC|_ denatured|denature|VBN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ ,|,|,|_ refolded|refold|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ 10x|10x|CD|_ RNA-structure|rna-structure|NN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 7.0|7.0|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ ,|,|,|_ 1|1|CD|_ M|m|NN|_ KCl|kcl|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ either|either|CC|_ 0.05|0.05|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ 2|2|CD|_ µg|µg|NN|_ RNase|rnase|NN|_ A|a|NN|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ stopped|stop|VBN|_ by|by|IN|_ extracting|extract|VBG|_ the|the|DT|_ RNA|rna|NN|_ with|with|IN|_ phenol-chlorophorm|phenol-chlorophorm|NN|_ .|.|.|_ The|the|DT|_ RNase|rnase|NN|_ A/T1-digested|a/t1-digested|JJ|_ sample|sample|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ with|with|IN|_ T4|t4|NN|_ PNK|pnk|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ purified|purify|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Both|both|CC|_ the|the|DT|_ V1|v1|NN|_ and|and|CC|_ A/T1|a/t1|NN|_ digested|digest|VBD|_ samples|sample|NNS|_ were|be|VBD|_ randomly|randomly|RB|_ fragmented|fragmented|JJ|_ in|in|IN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 9.2|9.2|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 12|12|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ .|.|.|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4103|mc4103|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Alexander|Alexander|NNP|_ ,|,|,|_ ,|,|,|_ Bartholomaeus|Bartholomaeus|NNP|_
Quality|Quality|NNP|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.2.1|1.2.1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 0.12.9|0.12.9|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 3|3|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Read|Read|NNP|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ the|the|DT|_ middle|middle|NN|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ the|the|DT|_ read|read|NN|_ count|count|NN|_ was|be|VBD|_ assigned|assign|VBN|_ to|to|TO|_ the|the|DT|_ nucleotide|nucleotide|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ see|see|VB|_ -LCB-|-lcb-|-LRB-|_ Kertesz|Kertesz|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RCB-|-rcb-|-RRB-|_ for|for|IN|_ details|detail|NNS|_
Read|Read|NNP|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ for|for|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ version|version|NN|_ U00096|u00096|NN|_ .2|.2|NN|_ ,|,|,|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Column|Column|NNP|_ 1|1|CD|_ names|name|NNS|_ the|the|DT|_ nucleotide|nucleotide|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ column|column|NN|_ 2|2|CD|_ gives|give|VBZ|_ counts|count|NNS|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ strand|strand|NN|_ ,|,|,|_ column|column|NN|_ 3|3|CD|_ for|for|IN|_ the|the|DT|_ reverse|reverse|JJ|_ strand|strand|NN|_ ,|,|,|_ columns|column|NNS|_ are|be|VBP|_ tab|tab|NN|_ separated|separated|JJ|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ enriched|enrich|VBN|_ in|in|IN|_ mRNA|mrna|NN|_ ,|,|,|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|genejet|NN|_ ™|™|NN|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ with|with|IN|_ two|two|CD|_ cycle|cycle|NN|_ of|of|IN|_ MICROBExpress|microbexpress|NN|_ ™|™|CD|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ probe|probe|VB|_ the|the|DT|_ RNA|rna|NN|_ structure|structure|NN|_ two|two|CD|_ µg|µg|NN|_ of|of|IN|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 45|45|CD|_ µl|µl|NN|_ of|of|IN|_ DEPC|depc|NN|_ water|water|NN|_ and|and|CC|_ denatured|denature|VBN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ ,|,|,|_ refolded|refold|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ 10x|10x|CD|_ RNA-structure|rna-structure|NN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 7.0|7.0|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ ,|,|,|_ 1|1|CD|_ M|m|NN|_ KCl|kcl|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ either|either|CC|_ 0.05|0.05|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ 2|2|CD|_ µg|µg|NN|_ RNase|rnase|NN|_ A|a|NN|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ stopped|stop|VBN|_ by|by|IN|_ extracting|extract|VBG|_ the|the|DT|_ RNA|rna|NN|_ with|with|IN|_ phenol-chlorophorm|phenol-chlorophorm|NN|_ .|.|.|_ The|the|DT|_ RNase|rnase|NN|_ A/T1-digested|a/t1-digested|JJ|_ sample|sample|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ with|with|IN|_ T4|t4|NN|_ PNK|pnk|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ purified|purify|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Both|both|CC|_ the|the|DT|_ V1|v1|NN|_ and|and|CC|_ A/T1|a/t1|NN|_ digested|digest|VBD|_ samples|sample|NNS|_ were|be|VBD|_ randomly|randomly|RB|_ fragmented|fragmented|JJ|_ in|in|IN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 9.2|9.2|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 12|12|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ .|.|.|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4107|mc4107|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ AT1|at1|NN|_ digested|digest|VBD|_ total|total|JJ|_ RNA|rna|NN|_
E.|e.|FW|_ coli|coli|FW|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Alexander|Alexander|NNP|_ ,|,|,|_ ,|,|,|_ Bartholomaeus|Bartholomaeus|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr1|delar1|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr1|delar1|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr1|delar1|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr1delAr2|delar1delar2|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr1delAr2|delar1delar2|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr1delAr2|delar1delar2|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr2|delar2|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr2|delar2|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr2|delar2|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|Crp|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|Crp|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|Crp|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|Crp|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|Crp|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|Crp|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|Crp|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|Crp|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|Crp|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ wt|wt|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ wt|wt|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ wt|wt|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ wt|wt|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ wt|wt|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ wt|wt|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
The|The|NNP|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ wt|wt|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Haythem|Haythem|NNP|_ ,|,|,|_ ,|,|,|_ Latif|Latif|NNP|_
GATC|GATC|NNP|_ software|software|NN|_ for|for|IN|_ read|read|NN|_ mapping|mapping|NN|_ on|on|IN|_ MG1655|mg1655|NN|_
verified|verify|VBN|_ with|with|IN|_ in-house|in-house|JJ|_ pipeline|pipeline|NN|_
Gene|gene|NN|_ wise|wise|JJ|_ natural|natural|JJ|_ spline|spline|NN|_ interpolation|interpolation|NN|_ of|of|IN|_ temporal|temporal|JJ|_ data|datum|NNS|_ from|from|IN|_ initial|initial|JJ|_ time|time|NN|_ points|point|NNS|_ to|to|TO|_ a|a|DT|_ dataset|dataset|NN|_ of|of|IN|_ 10|10|CD|_ minutes|minute|NNS|_ steps|step|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Expression|expression|NN|_ values|value|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ points|point|NNS|_ of|of|IN|_ the|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ are|be|VBP|_ not|not|RB|_ affected|affect|VBN|_ by|by|IN|_ the|the|DT|_ interpolation|interpolation|NN|_ .|.|.|_
gene|gene|NN|_ expression|expression|NN|_ sum|sum|NN|_ normalized|normalize|VBD|_ to|to|TO|_ 1|1|CD|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ time|time|NN|_ ,|,|,|_ rows|row|NNS|_ =|=|JJ|_ genes|gene|NNS|_ ,|,|,|_ cols|col|NNS|_ =|=|JJ|_ time|time|NN|_ points|point|NNS|_
RNA|rna|NN|_ extraction|extraction|NN|_ Kit|kit|NN|_
GATC|gatc|NN|_
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CSH50|csh50|NN|_
genotype|genotype|NN|_ :|:|:|_ wildtype|wildtype|JJ|_
time|time|NN|_ :|:|:|_ 60|60|CD|_ minutes|minute|NNS|_
LB|LB|NNP|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_
Patrick|Patrick|NNP|_ ,|,|,|_ ,|,|,|_ Sobetzko|Sobetzko|NNP|_
GATC|GATC|NNP|_ software|software|NN|_ for|for|IN|_ read|read|NN|_ mapping|mapping|NN|_ on|on|IN|_ MG1655|mg1655|NN|_
verified|verify|VBN|_ with|with|IN|_ in-house|in-house|JJ|_ pipeline|pipeline|NN|_
Gene|gene|NN|_ wise|wise|JJ|_ natural|natural|JJ|_ spline|spline|NN|_ interpolation|interpolation|NN|_ of|of|IN|_ temporal|temporal|JJ|_ data|datum|NNS|_ from|from|IN|_ initial|initial|JJ|_ time|time|NN|_ points|point|NNS|_ to|to|TO|_ a|a|DT|_ dataset|dataset|NN|_ of|of|IN|_ 10|10|CD|_ minutes|minute|NNS|_ steps|step|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Expression|expression|NN|_ values|value|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ points|point|NNS|_ of|of|IN|_ the|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ are|be|VBP|_ not|not|RB|_ affected|affect|VBN|_ by|by|IN|_ the|the|DT|_ interpolation|interpolation|NN|_ .|.|.|_
gene|gene|NN|_ expression|expression|NN|_ sum|sum|NN|_ normalized|normalize|VBD|_ to|to|TO|_ 1|1|CD|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ time|time|NN|_ ,|,|,|_ rows|row|NNS|_ =|=|JJ|_ genes|gene|NNS|_ ,|,|,|_ cols|col|NNS|_ =|=|JJ|_ time|time|NN|_ points|point|NNS|_
RNA|rna|NN|_ extraction|extraction|NN|_ Kit|kit|NN|_
GATC|gatc|NN|_
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δfis|δfis|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CSH50|csh50|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-fis|delta-fis|JJ|_
time|time|NN|_ :|:|:|_ 60|60|CD|_ minutes|minute|NNS|_
LB|LB|NNP|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δfis|Δfis|NNP|_
Patrick|Patrick|NNP|_ ,|,|,|_ ,|,|,|_ Sobetzko|Sobetzko|NNP|_
GATC|GATC|NNP|_ software|software|NN|_ for|for|IN|_ read|read|NN|_ mapping|mapping|NN|_ on|on|IN|_ MG1655|mg1655|NN|_
verified|verify|VBN|_ with|with|IN|_ in-house|in-house|JJ|_ pipeline|pipeline|NN|_
Gene|gene|NN|_ wise|wise|JJ|_ natural|natural|JJ|_ spline|spline|NN|_ interpolation|interpolation|NN|_ of|of|IN|_ temporal|temporal|JJ|_ data|datum|NNS|_ from|from|IN|_ initial|initial|JJ|_ time|time|NN|_ points|point|NNS|_ to|to|TO|_ a|a|DT|_ dataset|dataset|NN|_ of|of|IN|_ 10|10|CD|_ minutes|minute|NNS|_ steps|step|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Expression|expression|NN|_ values|value|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ points|point|NNS|_ of|of|IN|_ the|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ are|be|VBP|_ not|not|RB|_ affected|affect|VBN|_ by|by|IN|_ the|the|DT|_ interpolation|interpolation|NN|_ .|.|.|_
gene|gene|NN|_ expression|expression|NN|_ sum|sum|NN|_ normalized|normalize|VBD|_ to|to|TO|_ 1|1|CD|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ time|time|NN|_ ,|,|,|_ rows|row|NNS|_ =|=|JJ|_ genes|gene|NNS|_ ,|,|,|_ cols|col|NNS|_ =|=|JJ|_ time|time|NN|_ points|point|NNS|_
RNA|rna|NN|_ extraction|extraction|NN|_ Kit|kit|NN|_
GATC|gatc|NN|_
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δfis|δfis|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CSH50|csh50|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-fis|delta-fis|JJ|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ minutes|minute|NNS|_
LB|LB|NNP|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δfis|Δfis|NNP|_
Patrick|Patrick|NNP|_ ,|,|,|_ ,|,|,|_ Sobetzko|Sobetzko|NNP|_
GATC|GATC|NNP|_ software|software|NN|_ for|for|IN|_ read|read|NN|_ mapping|mapping|NN|_ on|on|IN|_ MG1655|mg1655|NN|_
verified|verify|VBN|_ with|with|IN|_ in-house|in-house|JJ|_ pipeline|pipeline|NN|_
Gene|gene|NN|_ wise|wise|JJ|_ natural|natural|JJ|_ spline|spline|NN|_ interpolation|interpolation|NN|_ of|of|IN|_ temporal|temporal|JJ|_ data|datum|NNS|_ from|from|IN|_ initial|initial|JJ|_ time|time|NN|_ points|point|NNS|_ to|to|TO|_ a|a|DT|_ dataset|dataset|NN|_ of|of|IN|_ 10|10|CD|_ minutes|minute|NNS|_ steps|step|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Expression|expression|NN|_ values|value|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ points|point|NNS|_ of|of|IN|_ the|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ are|be|VBP|_ not|not|RB|_ affected|affect|VBN|_ by|by|IN|_ the|the|DT|_ interpolation|interpolation|NN|_ .|.|.|_
gene|gene|NN|_ expression|expression|NN|_ sum|sum|NN|_ normalized|normalize|VBD|_ to|to|TO|_ 1|1|CD|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ time|time|NN|_ ,|,|,|_ rows|row|NNS|_ =|=|JJ|_ genes|gene|NNS|_ ,|,|,|_ cols|col|NNS|_ =|=|JJ|_ time|time|NN|_ points|point|NNS|_
RNA|rna|NN|_ extraction|extraction|NN|_ Kit|kit|NN|_
GATC|gatc|NN|_
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δfis|δfis|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CSH50|csh50|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-fis|delta-fis|JJ|_
time|time|NN|_ :|:|:|_ 180|180|CD|_ minutes|minute|NNS|_
LB|LB|NNP|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δfis|Δfis|NNP|_
Patrick|Patrick|NNP|_ ,|,|,|_ ,|,|,|_ Sobetzko|Sobetzko|NNP|_
GATC|GATC|NNP|_ software|software|NN|_ for|for|IN|_ read|read|NN|_ mapping|mapping|NN|_ on|on|IN|_ MG1655|mg1655|NN|_
verified|verify|VBN|_ with|with|IN|_ in-house|in-house|JJ|_ pipeline|pipeline|NN|_
Gene|gene|NN|_ wise|wise|JJ|_ natural|natural|JJ|_ spline|spline|NN|_ interpolation|interpolation|NN|_ of|of|IN|_ temporal|temporal|JJ|_ data|datum|NNS|_ from|from|IN|_ initial|initial|JJ|_ time|time|NN|_ points|point|NNS|_ to|to|TO|_ a|a|DT|_ dataset|dataset|NN|_ of|of|IN|_ 10|10|CD|_ minutes|minute|NNS|_ steps|step|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Expression|expression|NN|_ values|value|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ points|point|NNS|_ of|of|IN|_ the|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ are|be|VBP|_ not|not|RB|_ affected|affect|VBN|_ by|by|IN|_ the|the|DT|_ interpolation|interpolation|NN|_ .|.|.|_
gene|gene|NN|_ expression|expression|NN|_ sum|sum|NN|_ normalized|normalize|VBD|_ to|to|TO|_ 1|1|CD|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ time|time|NN|_ ,|,|,|_ rows|row|NNS|_ =|=|JJ|_ genes|gene|NNS|_ ,|,|,|_ cols|col|NNS|_ =|=|JJ|_ time|time|NN|_ points|point|NNS|_
RNA|rna|NN|_ extraction|extraction|NN|_ Kit|kit|NN|_
GATC|gatc|NN|_
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δfis|δfis|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CSH50|csh50|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-fis|delta-fis|JJ|_
time|time|NN|_ :|:|:|_ 420|420|CD|_ minutes|minute|NNS|_
LB|LB|NNP|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δfis|Δfis|NNP|_
Patrick|Patrick|NNP|_ ,|,|,|_ ,|,|,|_ Sobetzko|Sobetzko|NNP|_
GATC|GATC|NNP|_ software|software|NN|_ for|for|IN|_ read|read|NN|_ mapping|mapping|NN|_ on|on|IN|_ MG1655|mg1655|NN|_
verified|verify|VBN|_ with|with|IN|_ in-house|in-house|JJ|_ pipeline|pipeline|NN|_
Gene|gene|NN|_ wise|wise|JJ|_ natural|natural|JJ|_ spline|spline|NN|_ interpolation|interpolation|NN|_ of|of|IN|_ temporal|temporal|JJ|_ data|datum|NNS|_ from|from|IN|_ initial|initial|JJ|_ time|time|NN|_ points|point|NNS|_ to|to|TO|_ a|a|DT|_ dataset|dataset|NN|_ of|of|IN|_ 10|10|CD|_ minutes|minute|NNS|_ steps|step|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Expression|expression|NN|_ values|value|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ points|point|NNS|_ of|of|IN|_ the|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ are|be|VBP|_ not|not|RB|_ affected|affect|VBN|_ by|by|IN|_ the|the|DT|_ interpolation|interpolation|NN|_ .|.|.|_
gene|gene|NN|_ expression|expression|NN|_ sum|sum|NN|_ normalized|normalize|VBD|_ to|to|TO|_ 1|1|CD|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ time|time|NN|_ ,|,|,|_ rows|row|NNS|_ =|=|JJ|_ genes|gene|NNS|_ ,|,|,|_ cols|col|NNS|_ =|=|JJ|_ time|time|NN|_ points|point|NNS|_
RNA|rna|NN|_ extraction|extraction|NN|_ Kit|kit|NN|_
GATC|gatc|NN|_
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δhns|δhns|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CSH50|csh50|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-hns|delta-hn|NNS|_
time|time|NN|_ :|:|:|_ 60|60|CD|_ minutes|minute|NNS|_
LB|LB|NNP|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δhns|δhns|NNS|_
Patrick|Patrick|NNP|_ ,|,|,|_ ,|,|,|_ Sobetzko|Sobetzko|NNP|_
GATC|GATC|NNP|_ software|software|NN|_ for|for|IN|_ read|read|NN|_ mapping|mapping|NN|_ on|on|IN|_ MG1655|mg1655|NN|_
verified|verify|VBN|_ with|with|IN|_ in-house|in-house|JJ|_ pipeline|pipeline|NN|_
Gene|gene|NN|_ wise|wise|JJ|_ natural|natural|JJ|_ spline|spline|NN|_ interpolation|interpolation|NN|_ of|of|IN|_ temporal|temporal|JJ|_ data|datum|NNS|_ from|from|IN|_ initial|initial|JJ|_ time|time|NN|_ points|point|NNS|_ to|to|TO|_ a|a|DT|_ dataset|dataset|NN|_ of|of|IN|_ 10|10|CD|_ minutes|minute|NNS|_ steps|step|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Expression|expression|NN|_ values|value|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ points|point|NNS|_ of|of|IN|_ the|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ are|be|VBP|_ not|not|RB|_ affected|affect|VBN|_ by|by|IN|_ the|the|DT|_ interpolation|interpolation|NN|_ .|.|.|_
gene|gene|NN|_ expression|expression|NN|_ sum|sum|NN|_ normalized|normalize|VBD|_ to|to|TO|_ 1|1|CD|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ time|time|NN|_ ,|,|,|_ rows|row|NNS|_ =|=|JJ|_ genes|gene|NNS|_ ,|,|,|_ cols|col|NNS|_ =|=|JJ|_ time|time|NN|_ points|point|NNS|_
RNA|rna|NN|_ extraction|extraction|NN|_ Kit|kit|NN|_
GATC|gatc|NN|_
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δhns|δhns|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CSH50|csh50|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-hns|delta-hn|NNS|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ minutes|minute|NNS|_
LB|LB|NNP|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δhns|δhns|NNS|_
Patrick|Patrick|NNP|_ ,|,|,|_ ,|,|,|_ Sobetzko|Sobetzko|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ glucose|glucose|NN|SUPP
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ glucose|glucose|NN|SUPP
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ fructose|fructose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ fructose|fructose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ acetate|acetate|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ acetate|acetate|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ acetate|acetate|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ acetate|acetate|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ acetate|acetate|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ _|_|NN|_ acetate|acetate|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta|delta|NN|_ _|_|NN|_ cra|cra|NN|GEN
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ glucose|glucose|NN|SUPP
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta|delta|NN|_ _|_|NN|_ cra|cra|NN|GEN
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ glucose|glucose|NN|SUPP
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ fructose|fructose|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta|delta|NN|_ _|_|NN|_ cra|cra|NN|GEN
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ fructose|fructose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ fructose|fructose|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ fructose|fructose|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta|delta|NN|_ _|_|NN|_ cra|cra|NN|GEN
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ fructose|fructose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ fructose|fructose|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta|delta|NN|_ _|_|NN|_ cra|cra|NN|GEN
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ acetate|acetate|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta|delta|NN|_ _|_|NN|_ cra|cra|NN|GEN
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ acetate|acetate|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Δcra|δcra|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|wt|JJ|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|wt|JJ|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔoxyR|δoxyr|NN|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-oxyR|delta-oxyr|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔoxyR|δoxyr|NN|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔoxyR|δoxyr|NN|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-oxyR|delta-oxyr|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔoxyR|δoxyr|NN|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔsoxR|δsoxr|NN|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-soxR|delta-soxr|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔsoxR|δsoxr|NN|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔsoxS|δsoxs|NN|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-soxS|delta-soxs|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔsoxS|δsoxs|NN|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔsoxS|δsoxs|NN|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-soxS|delta-soxs|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔsoxS|δsoxs|NN|_ PQ|pq|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadE|δgade|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-gadE|delta-gade|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadE|δgade|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadE|δgade|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-gadE|delta-gade|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadE|δgade|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadW|δgadw|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-gadW|delta-gadw|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadW|δgadw|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadW|δgadw|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-gadW|delta-gadw|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadW|δgadw|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadX|δgadx|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-gadX|delta-gadx|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadX|δgadx|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadX|δgadx|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ delta-gadX|delta-gadx|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ΔgadX|δgadx|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.4|1.4|CD|_
All|all|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench5|workbench5|NN|_ with|with|IN|_ the|the|DT|_ length|length|NN|_ fraction|fraction|NN|_ of|of|IN|_ 0.9|0.9|CD|_ and|and|CC|_ the|the|DT|_ similarity|similarity|NN|_ of|of|IN|_ 0.99|0.99|CD|_ .|.|.|_
The|the|DT|_ expression|expression|NN|_ levels|level|NNS|_ were|be|VBD|_ based|base|VBN|_ upon|upon|IN|_ the|the|DT|_ RPKM|RPKM|NNP|_ metric|metric|JJ|_ obtained|obtain|VBN|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ manner|manner|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ RPKM|rpkm|NN|_ is|be|VBZ|_ generated|generate|VBN|_ by|by|IN|_ in-house|in-house|JJ|_ script|script|NN|_
From|from|IN|_ the|the|DT|_ cells|cell|NNS|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ ,|,|,|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAsnapTM|rnasnaptm|NN|_ method|method|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ethanol|ethanol|NN|_ precipitation|precipitation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ ribo-zeroTM|ribo-zerotm|JJ|_ magnetic|magnetic|JJ|_ kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA|rrna|NN|_ removal|removal|NN|_ was|be|VBD|_ confirmed|confirm|VBN|_ using|use|VBG|_ ExperionTM|experiontm|NN|_ system|system|NN|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ 4|4|CD|_ µg|µg|NN|_ of|of|IN|_ the|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ to|to|TO|_ sizes|size|NNS|_ of|of|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ using|use|VBG|_ RNA|rna|NN|_ fragmentation|fragmentation|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Grand|Grand|NNP|_ Island|Island|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
50|50|CD|_ ng|ng|NN|_ of|of|IN|_ the|the|DT|_ fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ sequencing|sequencing|NN|_ library|library|NN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ ®|®|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ LB|lb|NN|MED media|media|NNS|MED grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ overnight|overnight|JJ|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ fresh|fresh|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ and|and|CC|_ then|then|RB|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ nm|nm|NN|_ ~|~|NN|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
No|no|DT|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ LB|lb|NN|MED media|media|NNS|MED grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ overnight|overnight|JJ|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ fresh|fresh|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ and|and|CC|_ then|then|RB|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ nm|nm|NN|_ ~|~|NN|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
No|no|DT|_ treatment|treatment|NN|_
Byung-Kwan|Byung-Kwan|NNP|_ ,|,|,|_ ,|,|,|_ Cho|Cho|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.4|1.4|CD|_
All|all|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench5|workbench5|NN|_ with|with|IN|_ the|the|DT|_ length|length|NN|_ fraction|fraction|NN|_ of|of|IN|_ 0.9|0.9|CD|_ and|and|CC|_ the|the|DT|_ similarity|similarity|NN|_ of|of|IN|_ 0.99|0.99|CD|_ .|.|.|_
The|the|DT|_ expression|expression|NN|_ levels|level|NNS|_ were|be|VBD|_ based|base|VBN|_ upon|upon|IN|_ the|the|DT|_ RPKM|RPKM|NNP|_ metric|metric|JJ|_ obtained|obtain|VBN|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ manner|manner|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ RPKM|rpkm|NN|_ is|be|VBZ|_ generated|generate|VBN|_ by|by|IN|_ in-house|in-house|JJ|_ script|script|NN|_
From|from|IN|_ the|the|DT|_ cells|cell|NNS|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ ,|,|,|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAsnapTM|rnasnaptm|NN|_ method|method|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ethanol|ethanol|NN|_ precipitation|precipitation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ ribo-zeroTM|ribo-zerotm|JJ|_ magnetic|magnetic|JJ|_ kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA|rrna|NN|_ removal|removal|NN|_ was|be|VBD|_ confirmed|confirm|VBN|_ using|use|VBG|_ ExperionTM|experiontm|NN|_ system|system|NN|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ 4|4|CD|_ µg|µg|NN|_ of|of|IN|_ the|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ to|to|TO|_ sizes|size|NNS|_ of|of|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ using|use|VBG|_ RNA|rna|NN|_ fragmentation|fragmentation|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Grand|Grand|NNP|_ Island|Island|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
50|50|CD|_ ng|ng|NN|_ of|of|IN|_ the|the|DT|_ fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ sequencing|sequencing|NN|_ library|library|NN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ ®|®|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ LB|lb|NN|MED media|media|NNS|MED grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ overnight|overnight|JJ|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ fresh|fresh|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ and|and|CC|_ then|then|RB|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ nm|nm|NN|_ ~|~|NN|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
No|no|DT|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ LB|lb|NN|MED media|media|NNS|MED grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ overnight|overnight|JJ|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ fresh|fresh|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ and|and|CC|_ then|then|RB|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ nm|nm|NN|_ ~|~|NN|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
No|no|DT|_ treatment|treatment|NN|_
Byung-Kwan|Byung-Kwan|NNP|_ ,|,|,|_ ,|,|,|_ Cho|Cho|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 3|3|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 3|3|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 3|3|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 4|4|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 4|4|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|SYM|_ 5|5|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 5|5|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|SYM|_ 5|5|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 8|8|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 8|8|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 24|24|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 24|24|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 24|24|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 48|48|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 48|48|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 48|48|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 168|168|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 168|168|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 168|168|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 336|336|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 336|336|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 336|336|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 3|3|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 3|3|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 3|3|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 4|4|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 4|4|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|SYM|_ 5|5|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 5|5|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|SYM|_ 5|5|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 6|6|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 6|6|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 8|8|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 8|8|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 24|24|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 24|24|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 24|24|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 48|48|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 48|48|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 48|48|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 336|336|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 336|336|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 336|336|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 3|3|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 3|3|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 3|3|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 4|4|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 4|4|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|SYM|_ 5|5|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 5|5|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|SYM|_ 5|5|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 6|6|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 6|6|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 8|8|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 8|8|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 24|24|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 24|24|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 24|24|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 48|48|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 48|48|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 48|48|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 168|168|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 168|168|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 168|168|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 336|336|CD|_ hr|hr|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 336|336|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 336|336|CD|_ hr|hr|NN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 3|3|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 3|3|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 3|3|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 4|4|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 4|4|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|SYM|_ 5|5|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 5|5|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|SYM|_ 5|5|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 6|6|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 6|6|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 8|8|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 8|8|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 24|24|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 24|24|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 24|24|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 48|48|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 48|48|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 48|48|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 168|168|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 168|168|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 168|168|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
RNAsnap|rnasnap|NN|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 336|336|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 336|336|CD|_ hours|hour|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g/l|g/l|NN|_ -LRB-|-lrb-|-LRB-|_ DM500|dm500|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ To|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experiment|experiment|NN|_ ,|,|,|_ these|these|DT|_ preconditioned|preconditioned|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ DM500|dm500|CD|_ in|in|IN|_ multiple|multiple|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ until|until|IN|_ harvesting|harvesting|NN|_ cells|cell|NNS|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ All|all|DT|_ growth|growth|NN|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 120|120|CD|_ r.p.m.|r.p.m.|NN|_ over|over|IN|_ a|a|DT|_ one-inch|one-inch|JJ|_ diameter|diameter|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 336|336|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Jeffrey|Jeffrey|NNP|_ ,|,|,|_ E.|E.|NNP|_ ,|,|,|_ Barrick|Barrick|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
time|time|NN|_ :|:|:|_ 0.5|0.5|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
time|time|NN|_ :|:|:|_ 1|1|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
time|time|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
time|time|NN|_ :|:|:|_ 0.5|0.5|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
time|time|NN|_ :|:|:|_ 0.5|0.5|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
time|time|NN|_ :|:|:|_ 1|1|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
time|time|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -LRB-|-lrb-|-LRB-|_ 9.0|9.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Glucose|glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 15.0|15.0|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 2.2|2.2|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 0.55|0.55|CD|_ g/l|g/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaH2-Citrate|nah2-citrate|NN|_ -LRB-|-lrb-|-LRB-|_ 234|234|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ FeCl3|fecl3|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 25.0|25.0|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ZnSO4|znso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MnSO4|mnso4|NN|_ *|*|SYM|_ 7|7|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CuSO4|cuso4|NN|_ *|*|SYM|_ 5|5|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.16|0.16|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CoCl2|cocl2|NN|_ *|*|SYM|_ 6|6|CD|_ H2O|h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 0.18|0.18|CD|_ mg/l|mg/l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
batch|batch|NN|_ culture|culture|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l/min|l/min|NN|_ when|when|WRB|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600nm|600nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 3|3|CD|_ .|.|.|_
Joachim|Joachim|NNP|_ ,|,|,|_ ,|,|,|_ von|von|NNP|_ Wulffen|Wulffen|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|NN|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ LB|LB|NNP|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ LB|LB|NNP|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysG|cysg|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ cysG|cysg|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysG|cysg|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysH|cysh|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ cysH|cysh|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysH|cysh|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysH|cysh|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ cysH|cysh|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysH|cysh|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ dcd|dcd|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ dcd|dcd|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ dcd|dcd|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ dcd|dcd|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ dcd|dcd|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ dcd|dcd|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fadR|fadr|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ fadR|fadr|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fadR|fadr|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fadR|fadr|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ fadR|fadr|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fadR|fadr|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ppk|ppk|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ ppk|ppk|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ppk|ppk|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ wzc|wzc|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wzc|wzc|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ wzc|wzc|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ wzc|wzc|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wzc|wzc|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ wzc|wzc|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ yghD|yghd|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ yghD|yghd|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ yghD|yghd|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fepA|fepa|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ fepA|fepa|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fepA|fepa|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lacA|laca|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ lacA|laca|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lacA|laca|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ dcd|dcd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ dcd|dcd|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ dcd|dcd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ dcd|dcd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ dcd|dcd|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ dcd|dcd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fadR|fadr|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ fadR|fadr|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fadR|fadr|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fadR|fadr|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ fadR|fadr|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fadR|fadr|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ppk|ppk|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ ppk|ppk|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ppk|ppk|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ppk|ppk|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ ppk|ppk|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ppk|ppk|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ wzc|wzc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wzc|wzc|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ wzc|wzc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ wzc|wzc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wzc|wzc|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ wzc|wzc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ yghD|yghd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ yghD|yghd|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ yghD|yghd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ yghD|yghd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ yghD|yghd|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ yghD|yghd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fepA|fepa|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ fepA|fepa|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fepA|fepa|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mgtA|mgta|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ mgtA|mgta|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mgtA|mgta|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mgtA|mgta|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ mgtA|mgta|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mgtA|mgta|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ gabT|gabt|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ gabT|gabt|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ gabT|gabt|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ gabT|gabt|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ gabT|gabt|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ gabT|gabt|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ sdhC|sdhc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ sdhC|sdhc|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ sdhC|sdhc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ sdhC|sdhc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ sdhC|sdhc|NN|GEN knockout|knockout|JJ|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ sdhC|sdhc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ putP|putp|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ putP|putp|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ putP|putp|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ putP|putp|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ putP|putp|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ putP|putp|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ rfbA|rfba|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ rfbA|rfba|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ rfbA|rfba|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ rfbA|rfba|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ rfbA|rfba|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ rfbA|rfba|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ entF|entf|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ entF|entf|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ entF|entf|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ entF|entf|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ entF|entf|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ entF|entf|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ entF|entf|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ entF|entf|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ entF|entf|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ kefB|kefb|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ kefB|kefb|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ kefB|kefb|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ kefB|kefb|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ kefB|kefb|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ kefB|kefb|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysA|cysa|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ cysA|cysa|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysA|cysa|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysA|cysa|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ cysA|cysa|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysA|cysa|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysA|cysa|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ cysA|cysa|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysA|cysa|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ galE|gale|NN|GEN KO|KO|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ galE|gale|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ galE|gale|NN|GEN KO|KO|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mhpD|mhpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ mhpD|mhpd|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mhpD|mhpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mhpD|mhpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ mhpD|mhpd|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mhpD|mhpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mhpD|mhpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ mhpD|mhpd|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mhpD|mhpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fliY|fliy|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ fliY|fliy|NN|_ knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fliY|fliy|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fliY|fliy|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ fliY|fliy|NN|_ knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fliY|fliy|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fliY|fliy|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ fliY|fliy|NN|_ knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fliY|fliy|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lplA|lpla|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ lplA|lpla|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lplA|lpla|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lplA|lpla|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ lplA|lpla|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lplA|lpla|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lplA|lpla|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ lplA|lpla|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lplA|lpla|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ khc|khc|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ khc|khc|NN|_ knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ khc|khc|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ khc|khc|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ khc|khc|NN|_ knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ khc|khc|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ khc|khc|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ khc|khc|NN|_ knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ khc|khc|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ugpC|ugpc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ ugpC|ugpc|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ugpC|ugpc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ugpC|ugpc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ ugpC|ugpc|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ugpC|ugpc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ugpC|ugpc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ ugpC|ugpc|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ugpC|ugpc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ trpD|trpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ trpD|trpd|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ trpD|trpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ trpD|trpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ trpD|trpd|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ trpD|trpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ trpD|trpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ trpD|trpd|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ trpD|trpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ aspC|aspc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ aspC|aspc|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ aspC|aspc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ aspC|aspc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ aspC|aspc|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ aspC|aspc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
For|for|IN|_ RNA-Seq|rna-seq|JJ|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ aspC|aspc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
strain/background|strain/background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ aspC|aspc|NN|GEN knockout|knockout|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB/M9|lb/m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ At|at|IN|_ 12|12|CD|_ h|h|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ second|second|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ aspC|aspC|NNP|GEN _|_|SYM|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ M9|m9|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP was|be|VBD|_ done|do|VBN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ late|late|JJ|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase was|be|VBD|_ reached|reach|VBN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ aspC|aspc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Ilias|Ilias|NNP|_ ,|,|,|_ ,|,|,|_ Tagkopoulos|Tagkopoulos|NNP|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
All|All|NNP|_ raw|raw|JJ|_ FastQ|fastq|NN|_ files|file|NNS|_ generated|generate|VBN|_ were|be|VBD|_ filtered|filter|VBN|_ using|use|VBG|_ FASTX-Toolkit|fastx-toolkit|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit/|http://hannonlab.cshl.edu/fastx_toolkit/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ model|model|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ a|a|DT|_ normalized|normalize|VBN|_ metric|metric|JJ|_ to|to|TO|_ present|present|VB|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ levels|level|NNS|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ Nature|Nature|NNP|_ methods|method|NNS|_ 2008|2008|CD|_ ,|,|,|_ 5|5|CD|_ :|:|:|_ 621-628|621-628|CD|_ -RRB-|-rrb-|-RRB-|_
Transcripts|transcript|NNS|_ evaluation|evaluation|NN|_ of|of|IN|_ differential|differential|JJ|_ expression|expression|NN|_ were|be|VBD|_ accomplished|accomplish|VBN|_ using|use|VBG|_ MARS|mars|NN|_ -LRB-|-lrb-|-LRB-|_ MA-plot-based|ma-plot-based|JJ|_ method|method|NN|_ with|with|IN|_ Random|Random|NNP|_ sampling|sampling|NN|_ model|model|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ DEGseq|degseq|NN|_ package|package|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ Bioinformatics|bioinformatic|NNS|_ 2010|2010|CD|_ ,|,|,|_ 26|26|CD|_ :|:|:|_ 136-138|136-138|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655.2|002655.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ RPKM|rpkm|NN|_
RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RiboPure-BacteriaTM|RiboPure-BacteriaTM|NNP|_ Bacteria|bacterium|NNS|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ eliminate|eliminate|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommendations|recommendation|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ bacteria|bacterium|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.8|0.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Enterohemorrhagic|enterohemorrhagic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_
The|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ ×|×|CD|_ g|g|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ then|then|RB|_ washed|wash|VBN|_ with|with|IN|_ PBS|PBS|NNP|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
phase|phase|NN|_ :|:|:|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ bacteria|bacterium|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.8|0.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Enterohemorrhagic|enterohemorrhagic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_
The|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ ×|×|CD|_ g|g|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ then|then|RB|_ washed|wash|VBN|_ with|with|IN|_ PBS|PBS|NNP|_ .|.|.|_
Baoshan|Baoshan|NNP|_ ,|,|,|_ ,|,|,|_ Wan|Wan|NNP|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
All|All|NNP|_ raw|raw|JJ|_ FastQ|fastq|NN|_ files|file|NNS|_ generated|generate|VBN|_ were|be|VBD|_ filtered|filter|VBN|_ using|use|VBG|_ FASTX-Toolkit|fastx-toolkit|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit/|http://hannonlab.cshl.edu/fastx_toolkit/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ model|model|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ a|a|DT|_ normalized|normalize|VBN|_ metric|metric|JJ|_ to|to|TO|_ present|present|VB|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ levels|level|NNS|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ Nature|Nature|NNP|_ methods|method|NNS|_ 2008|2008|CD|_ ,|,|,|_ 5|5|CD|_ :|:|:|_ 621-628|621-628|CD|_ -RRB-|-rrb-|-RRB-|_
Transcripts|transcript|NNS|_ evaluation|evaluation|NN|_ of|of|IN|_ differential|differential|JJ|_ expression|expression|NN|_ were|be|VBD|_ accomplished|accomplish|VBN|_ using|use|VBG|_ MARS|mars|NN|_ -LRB-|-lrb-|-LRB-|_ MA-plot-based|ma-plot-based|JJ|_ method|method|NN|_ with|with|IN|_ Random|Random|NNP|_ sampling|sampling|NN|_ model|model|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ DEGseq|degseq|NN|_ package|package|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ Bioinformatics|bioinformatic|NNS|_ 2010|2010|CD|_ ,|,|,|_ 26|26|CD|_ :|:|:|_ 136-138|136-138|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655.2|002655.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ RPKM|rpkm|NN|_
RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RiboPure-BacteriaTM|RiboPure-BacteriaTM|NNP|_ Bacteria|bacterium|NNS|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ eliminate|eliminate|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommendations|recommendation|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ bacteria|bacterium|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.8|0.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Enterohemorrhagic|enterohemorrhagic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_
The|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ ×|×|CD|_ g|g|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ then|then|RB|_ washed|wash|VBN|_ with|with|IN|_ PBS|PBS|NNP|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
phase|phase|NN|_ :|:|:|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ bacteria|bacterium|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.8|0.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Enterohemorrhagic|enterohemorrhagic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_
The|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ ×|×|CD|_ g|g|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ then|then|RB|_ washed|wash|VBN|_ with|with|IN|_ PBS|PBS|NNP|_ .|.|.|_
Baoshan|Baoshan|NNP|_ ,|,|,|_ ,|,|,|_ Wan|Wan|NNP|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
All|All|NNP|_ raw|raw|JJ|_ FastQ|fastq|NN|_ files|file|NNS|_ generated|generate|VBN|_ were|be|VBD|_ filtered|filter|VBN|_ using|use|VBG|_ FASTX-Toolkit|fastx-toolkit|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit/|http://hannonlab.cshl.edu/fastx_toolkit/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ model|model|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ a|a|DT|_ normalized|normalize|VBN|_ metric|metric|JJ|_ to|to|TO|_ present|present|VB|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ levels|level|NNS|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ Nature|Nature|NNP|_ methods|method|NNS|_ 2008|2008|CD|_ ,|,|,|_ 5|5|CD|_ :|:|:|_ 621-628|621-628|CD|_ -RRB-|-rrb-|-RRB-|_
Transcripts|transcript|NNS|_ evaluation|evaluation|NN|_ of|of|IN|_ differential|differential|JJ|_ expression|expression|NN|_ were|be|VBD|_ accomplished|accomplish|VBN|_ using|use|VBG|_ MARS|mars|NN|_ -LRB-|-lrb-|-LRB-|_ MA-plot-based|ma-plot-based|JJ|_ method|method|NN|_ with|with|IN|_ Random|Random|NNP|_ sampling|sampling|NN|_ model|model|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ DEGseq|degseq|NN|_ package|package|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ Bioinformatics|bioinformatic|NNS|_ 2010|2010|CD|_ ,|,|,|_ 26|26|CD|_ :|:|:|_ 136-138|136-138|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655.2|002655.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ RPKM|rpkm|NN|_
RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RiboPure-BacteriaTM|RiboPure-BacteriaTM|NNP|_ Bacteria|bacterium|NNS|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ eliminate|eliminate|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommendations|recommendation|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ bacteria|bacterium|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.8|0.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Enterohemorrhagic|enterohemorrhagic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_
The|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ ×|×|CD|_ g|g|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ then|then|RB|_ washed|wash|VBN|_ with|with|IN|_ PBS|PBS|NNP|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ hns|hn|VBZ|GEN
phase|phase|NN|_ :|:|:|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ bacteria|bacterium|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.8|0.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Enterohemorrhagic|enterohemorrhagic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_
The|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ ×|×|CD|_ g|g|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ then|then|RB|_ washed|wash|VBN|_ with|with|IN|_ PBS|PBS|NNP|_ .|.|.|_
Baoshan|Baoshan|NNP|_ ,|,|,|_ ,|,|,|_ Wan|Wan|NNP|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
All|All|NNP|_ raw|raw|JJ|_ FastQ|fastq|NN|_ files|file|NNS|_ generated|generate|VBN|_ were|be|VBD|_ filtered|filter|VBN|_ using|use|VBG|_ FASTX-Toolkit|fastx-toolkit|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit/|http://hannonlab.cshl.edu/fastx_toolkit/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ model|model|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ a|a|DT|_ normalized|normalize|VBN|_ metric|metric|JJ|_ to|to|TO|_ present|present|VB|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ levels|level|NNS|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ Nature|Nature|NNP|_ methods|method|NNS|_ 2008|2008|CD|_ ,|,|,|_ 5|5|CD|_ :|:|:|_ 621-628|621-628|CD|_ -RRB-|-rrb-|-RRB-|_
Transcripts|transcript|NNS|_ evaluation|evaluation|NN|_ of|of|IN|_ differential|differential|JJ|_ expression|expression|NN|_ were|be|VBD|_ accomplished|accomplish|VBN|_ using|use|VBG|_ MARS|mars|NN|_ -LRB-|-lrb-|-LRB-|_ MA-plot-based|ma-plot-based|JJ|_ method|method|NN|_ with|with|IN|_ Random|Random|NNP|_ sampling|sampling|NN|_ model|model|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ DEGseq|degseq|NN|_ package|package|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ Bioinformatics|bioinformatic|NNS|_ 2010|2010|CD|_ ,|,|,|_ 26|26|CD|_ :|:|:|_ 136-138|136-138|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655.2|002655.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ RPKM|rpkm|NN|_
RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RiboPure-BacteriaTM|RiboPure-BacteriaTM|NNP|_ Bacteria|bacterium|NNS|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ eliminate|eliminate|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommendations|recommendation|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ bacteria|bacterium|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.8|0.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Enterohemorrhagic|enterohemorrhagic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_
The|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ ×|×|CD|_ g|g|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ then|then|RB|_ washed|wash|VBN|_ with|with|IN|_ PBS|PBS|NNP|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ hns|hn|VBZ|GEN
phase|phase|NN|_ :|:|:|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ bacteria|bacterium|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.8|0.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Enterohemorrhagic|enterohemorrhagic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_
The|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ ×|×|CD|_ g|g|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ then|then|RB|_ washed|wash|VBN|_ with|with|IN|_ PBS|PBS|NNP|_ .|.|.|_
Baoshan|Baoshan|NNP|_ ,|,|,|_ ,|,|,|_ Wan|Wan|NNP|_
Raw|raw|NN|_ sequence|sequence|NN|_ data|datum|NNS|_ obtained|obtain|VBN|_ in|in|IN|_ the|the|DT|_ fastq|fastq|NN|_ format|format|NN|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ matching|match|VBG|_ program|program|NN|_ BWA|bwa|NN|_ .|.|.|_ Reads|read|NNS|_ mapping|map|VBG|_ uniquely|uniquely|RB|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ selected|select|VBN|_ and|and|CC|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ computed|compute|VBN|_ using|use|VBG|_ custom|custom|NN|_ scripts|script|NNS|_ .|.|.|_
These|these|DT|_ counts|count|NNS|_ were|be|VBD|_ fed|feed|VBN|_ into|into|IN|_ the|the|DT|_ DESeq|deseq|NN|_ package|package|NN|_ in|in|IN|_ Bioconductor|Bioconductor|NNP|_ to|to|TO|_ estimate|estimate|VB|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ mutants|mutant|NNS|_ and|and|CC|_ the|the|DT|_ wildtype|wildtype|JJ|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ ;|;|:|_ genes|gene|NNS|_ in|in|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ in|in|IN|_ columns|column|NNS|_ ;|;|:|_ each|each|DT|_ entry|entry|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ the|the|DT|_ given|give|VBN|_ gene|gene|NN|_ in|in|IN|_ the|the|DT|_ given|give|VBN|_ sample|sample|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ DNAse|dnase|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 18068-015|18068-015|CD|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Further|further|JJ|_ precipitation|precipitation|NN|_ of|of|IN|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ cleanup|cleanup|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ cat|cat|NN|_ .|.|.|_ no|no|DT|_ .|.|.|_ AM1905|am1905|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ finally|finally|RB|_ suspended|suspend|VBN|_ in|in|IN|_ 10|10|CD|_ μL|μl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ .|.|.|_
Libraries|Libraries|NNPS|_ for|for|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 1000|1000|CD|_ sequencing|sequencing|NN|_ using|use|VBG|_ the|the|DT|_ Truseq|Truseq|NNP|_ kit|kit|NN|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ protocols|protocol|NNS|_ recommended|recommend|VBN|_ by|by|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ .|.|.|_
M9|m9|NN|_ defined|define|VBN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 0.6|0.6|CD|_ %|%|NN|_ Na2HPO4|na2hpo4|NN|_ ,|,|,|_ 0.3|0.3|CD|_ %|%|NN|_ KH2PO4|kh2po4|NN|_ ,|,|,|_ 0.05|0.05|CD|_ %|%|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 0.01|0.01|CD|_ %|%|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ 5|5|CD|_ x|x|CC|_ 10|10|CD|_ −|−|NN|_ 4|4|CD|_ %|%|NN|_ Thiamin|thiamin|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.1|0.1|CD|_ %|%|NN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP was|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 100|100|CD|_ mL|ml|NN|_ fresh|fresh|JJ|_ M9|m9|NN|_ glucose|glucose|NN|SUPP to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ .|.|.|_ The|the|DT|_ flasks|flask|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mid-exponential|mid-exponential|JJ|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transition|transition|NN|_ to|to|TO|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ 16|16|CD|_ hrs|hr|NNS|_ ,|,|,|_ OD600|od600|NN|_ ~|~|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ late|late|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ 48|48|CD|_ hrs|hr|NNS|_ ,|,|,|_ OD600|od600|NN|_ ~|~|NN|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ phases|phase|NNS|_ of|of|IN|_ growth|growth|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ del|del|DT|_ rpoS|rpos|NN|GEN
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Transition|transition|NN|_ to|to|TO|_ Stationary|stationary|JJ|_
M9|m9|NN|_ defined|define|VBN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 0.6|0.6|CD|_ %|%|NN|_ Na2HPO4|na2hpo4|NN|_ ,|,|,|_ 0.3|0.3|CD|_ %|%|NN|_ KH2PO4|kh2po4|NN|_ ,|,|,|_ 0.05|0.05|CD|_ %|%|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 0.01|0.01|CD|_ %|%|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ 5|5|CD|_ x|x|CC|_ 10|10|CD|_ −|−|NN|_ 4|4|CD|_ %|%|NN|_ Thiamin|thiamin|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.1|0.1|CD|_ %|%|NN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP was|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 100|100|CD|_ mL|ml|NN|_ fresh|fresh|JJ|_ M9|m9|NN|_ glucose|glucose|NN|SUPP to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ .|.|.|_ The|the|DT|_ flasks|flask|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mid-exponential|mid-exponential|JJ|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transition|transition|NN|_ to|to|TO|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ 16|16|CD|_ hrs|hr|NNS|_ ,|,|,|_ OD600|od600|NN|_ ~|~|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ late|late|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ 48|48|CD|_ hrs|hr|NNS|_ ,|,|,|_ OD600|od600|NN|_ ~|~|NN|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ phases|phase|NNS|_ of|of|IN|_ growth|growth|NN|_ .|.|.|_
Avantika|Avantika|NNP|_ ,|,|,|_ ,|,|,|_ Lal|Lal|NNP|_
Raw|raw|NN|_ sequence|sequence|NN|_ data|datum|NNS|_ obtained|obtain|VBN|_ in|in|IN|_ the|the|DT|_ fastq|fastq|NN|_ format|format|NN|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ matching|match|VBG|_ program|program|NN|_ BWA|bwa|NN|_ .|.|.|_ Reads|read|NNS|_ mapping|map|VBG|_ uniquely|uniquely|RB|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ selected|select|VBN|_ and|and|CC|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ computed|compute|VBN|_ using|use|VBG|_ custom|custom|NN|_ scripts|script|NNS|_ .|.|.|_
These|these|DT|_ counts|count|NNS|_ were|be|VBD|_ fed|feed|VBN|_ into|into|IN|_ the|the|DT|_ DESeq|deseq|NN|_ package|package|NN|_ in|in|IN|_ Bioconductor|Bioconductor|NNP|_ to|to|TO|_ estimate|estimate|VB|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ mutants|mutant|NNS|_ and|and|CC|_ the|the|DT|_ wildtype|wildtype|JJ|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ ;|;|:|_ genes|gene|NNS|_ in|in|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ in|in|IN|_ columns|column|NNS|_ ;|;|:|_ each|each|DT|_ entry|entry|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ the|the|DT|_ given|give|VBN|_ gene|gene|NN|_ in|in|IN|_ the|the|DT|_ given|give|VBN|_ sample|sample|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ DNAse|dnase|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 18068-015|18068-015|CD|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ Further|further|JJ|_ precipitation|precipitation|NN|_ of|of|IN|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ cleanup|cleanup|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ cat|cat|NN|_ .|.|.|_ no|no|DT|_ .|.|.|_ AM1905|am1905|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ finally|finally|RB|_ suspended|suspend|VBN|_ in|in|IN|_ 10|10|CD|_ μL|μl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ .|.|.|_
Libraries|Libraries|NNPS|_ for|for|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 1000|1000|CD|_ sequencing|sequencing|NN|_ using|use|VBG|_ the|the|DT|_ Truseq|Truseq|NNP|_ kit|kit|NN|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ protocols|protocol|NNS|_ recommended|recommend|VBN|_ by|by|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ .|.|.|_
M9|m9|NN|_ defined|define|VBN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 0.6|0.6|CD|_ %|%|NN|_ Na2HPO4|na2hpo4|NN|_ ,|,|,|_ 0.3|0.3|CD|_ %|%|NN|_ KH2PO4|kh2po4|NN|_ ,|,|,|_ 0.05|0.05|CD|_ %|%|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 0.01|0.01|CD|_ %|%|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ 5|5|CD|_ x|x|CC|_ 10|10|CD|_ −|−|NN|_ 4|4|CD|_ %|%|NN|_ Thiamin|thiamin|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.1|0.1|CD|_ %|%|NN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP was|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 100|100|CD|_ mL|ml|NN|_ fresh|fresh|JJ|_ M9|m9|NN|_ glucose|glucose|NN|SUPP to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ .|.|.|_ The|the|DT|_ flasks|flask|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mid-exponential|mid-exponential|JJ|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transition|transition|NN|_ to|to|TO|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ 16|16|CD|_ hrs|hr|NNS|_ ,|,|,|_ OD600|od600|NN|_ ~|~|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ late|late|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ 48|48|CD|_ hrs|hr|NNS|_ ,|,|,|_ OD600|od600|NN|_ ~|~|NN|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ phases|phase|NNS|_ of|of|IN|_ growth|growth|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ del|del|DT|_ ssrS|ssrs|NN|GEN
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ Stationary|stationary|JJ|_
M9|m9|NN|_ defined|define|VBN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 0.6|0.6|CD|_ %|%|NN|_ Na2HPO4|na2hpo4|NN|_ ,|,|,|_ 0.3|0.3|CD|_ %|%|NN|_ KH2PO4|kh2po4|NN|_ ,|,|,|_ 0.05|0.05|CD|_ %|%|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 0.01|0.01|CD|_ %|%|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ 5|5|CD|_ x|x|CC|_ 10|10|CD|_ −|−|NN|_ 4|4|CD|_ %|%|NN|_ Thiamin|thiamin|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.1|0.1|CD|_ %|%|NN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP was|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 100|100|CD|_ mL|ml|NN|_ fresh|fresh|JJ|_ M9|m9|NN|_ glucose|glucose|NN|SUPP to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ .|.|.|_ The|the|DT|_ flasks|flask|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mid-exponential|mid-exponential|JJ|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transition|transition|NN|_ to|to|TO|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ 16|16|CD|_ hrs|hr|NNS|_ ,|,|,|_ OD600|od600|NN|_ ~|~|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ late|late|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ 48|48|CD|_ hrs|hr|NNS|_ ,|,|,|_ OD600|od600|NN|_ ~|~|NN|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ phases|phase|NNS|_ of|of|IN|_ growth|growth|NN|_ .|.|.|_
Avantika|Avantika|NNP|_ ,|,|,|_ ,|,|,|_ Lal|Lal|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WT|WT|NNP|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WTKas|wtka|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WTKas|wtka|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WTKas|wtka|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WTKas|wtka|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WTKas|wtka|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WTKas|wtka|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WTKas|wtka|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WTKas|wtka|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ WTKas|wtka|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ Mut|mut|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ neo|neo|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ neo|neo|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 1|1|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ neo|neo|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ neo|neo|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ neo|neo|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ neo|neo|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ neo|neo|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ neo|neo|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ bla|bla|FW|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ bla|bla|FW|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 1|1|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ bla|bla|FW|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ bla|bla|FW|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ bla|bla|FW|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ bla|bla|FW|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ bla|bla|FW|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ bla|bla|FW|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ mMaple3|mmaple3|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ mMaple3|mmaple3|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 1|1|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ mMaple3|mmaple3|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ mMaple3|mmaple3|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ mMaple3|mmaple3|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ mMaple3|mmaple3|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ mMaple3|mmaple3|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ mMaple3|mmaple3|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ phoA|phoa|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ phoA|phoa|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 1|1|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ phoA|phoa|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ phoA|phoa|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ phoA|phoa|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ phoA|phoa|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ phoA|phoa|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ phoA|phoa|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ lacZ|lacz|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ lacZ|lacz|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 1|1|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ lacZ|lacz|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ lacZ|lacz|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ lacZ|lacz|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ lacZ|lacz|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ lacZ|lacz|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
csv|csv|JJ|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA/D/G|spka/d/g|NN|_ /|/|:|_ K|K|NNP|_ represent|represent|VBP|_ spike|spike|NN|_ in|in|IN|_ control|control|NN|_ molecules|molecule|NNS|_ used|use|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ fusion|fusion|NN|_ RNAs|rna|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype/variaion|genotype/variaion|NN|_ :|:|:|_ lacZ|lacz|NN|GEN
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mg1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
Xiaowei|Xiaowei|NNP|_ ,|,|,|_ ,|,|,|_ Zhuang|Zhuang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ HCS|hcs|NN|_ 2.0.5|2.0.5|CD|_ and|and|CC|_ RTA|RTA|NNP|_ 1.17.20|1.17.20|CD|_
RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ 1.8.2|1.8.2|CD|_
Gene|Gene|NNP|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ based|base|VBN|_ on|on|IN|_ known|known|JJ|_ genes|gene|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ 2.0.2|2.0.2|CD|_ ,|,|,|_ only|only|RB|_ PF|pf|NN|_ reads|read|VBZ|_ were|be|VBD|_ retained|retain|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 007779|007779|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ with|with|IN|_ coverage|coverage|NN|_ and|and|CC|_ FPKM|fpkm|NN|_ measurements|measurement|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ frozen|frozen|JJ|_ acid-phenol|acid-phenol|NN|_ method|method|NN|_ described|describe|VBN|_ by|by|IN|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ -LRB-|-lrb-|-LRB-|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ ,|,|,|_ 1992|1992|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNaseI|dnasei|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ ScriptseqTM|ScriptseqTM|NNP|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ preparation|preparation|NN|_ kit|kit|NN|_ with|with|IN|_ 50|50|CD|_ ng|ng|NN|_ of|of|IN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ ;|;|:|_ Strand|Strand|NNP|_ orientated|orientate|VBD|_ RNA-Seq|rna-seq|JJ|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ control|control|NN|_ condition|condition|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ control|control|NN|_ condition|condition|NN|_
Agnès|Agnès|NNP|_ ,|,|,|_ ,|,|,|_ Rodrigue|Rodrigue|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ HCS|hcs|NN|_ 2.0.5|2.0.5|CD|_ and|and|CC|_ RTA|RTA|NNP|_ 1.17.20|1.17.20|CD|_
RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ 1.8.2|1.8.2|CD|_
Gene|Gene|NNP|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ based|base|VBN|_ on|on|IN|_ known|known|JJ|_ genes|gene|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ 2.0.2|2.0.2|CD|_ ,|,|,|_ only|only|RB|_ PF|pf|NN|_ reads|read|VBZ|_ were|be|VBD|_ retained|retain|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 007779|007779|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ with|with|IN|_ coverage|coverage|NN|_ and|and|CC|_ FPKM|fpkm|NN|_ measurements|measurement|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ frozen|frozen|JJ|_ acid-phenol|acid-phenol|NN|_ method|method|NN|_ described|describe|VBN|_ by|by|IN|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ -LRB-|-lrb-|-LRB-|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ ,|,|,|_ 1992|1992|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNaseI|dnasei|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ ScriptseqTM|ScriptseqTM|NNP|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ preparation|preparation|NN|_ kit|kit|NN|_ with|with|IN|_ 50|50|CD|_ ng|ng|NN|_ of|of|IN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ ;|;|:|_ Strand|Strand|NNP|_ orientated|orientate|VBD|_ RNA-Seq|rna-seq|JJ|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ control|control|NN|_ condition|condition|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ control|control|NN|_ condition|condition|NN|_
Agnès|Agnès|NNP|_ ,|,|,|_ ,|,|,|_ Rodrigue|Rodrigue|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ HCS|hcs|NN|_ 2.0.5|2.0.5|CD|_ and|and|CC|_ RTA|RTA|NNP|_ 1.17.20|1.17.20|CD|_
RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ 1.8.2|1.8.2|CD|_
Gene|Gene|NNP|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ based|base|VBN|_ on|on|IN|_ known|known|JJ|_ genes|gene|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ 2.0.2|2.0.2|CD|_ ,|,|,|_ only|only|RB|_ PF|pf|NN|_ reads|read|VBZ|_ were|be|VBD|_ retained|retain|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 007779|007779|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ with|with|IN|_ coverage|coverage|NN|_ and|and|CC|_ FPKM|fpkm|NN|_ measurements|measurement|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ frozen|frozen|JJ|_ acid-phenol|acid-phenol|NN|_ method|method|NN|_ described|describe|VBN|_ by|by|IN|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ -LRB-|-lrb-|-LRB-|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ ,|,|,|_ 1992|1992|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNaseI|dnasei|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ ScriptseqTM|ScriptseqTM|NNP|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ preparation|preparation|NN|_ kit|kit|NN|_ with|with|IN|_ 50|50|CD|_ ng|ng|NN|_ of|of|IN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ ;|;|:|_ Strand|Strand|NNP|_ orientated|orientate|VBD|_ RNA-Seq|rna-seq|JJ|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ control|control|NN|_ condition|condition|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ control|control|NN|_ condition|condition|NN|_
Agnès|Agnès|NNP|_ ,|,|,|_ ,|,|,|_ Rodrigue|Rodrigue|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ HCS|hcs|NN|_ 2.0.5|2.0.5|CD|_ and|and|CC|_ RTA|RTA|NNP|_ 1.17.20|1.17.20|CD|_
RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ 1.8.2|1.8.2|CD|_
Gene|Gene|NNP|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ based|base|VBN|_ on|on|IN|_ known|known|JJ|_ genes|gene|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ 2.0.2|2.0.2|CD|_ ,|,|,|_ only|only|RB|_ PF|pf|NN|_ reads|read|VBZ|_ were|be|VBD|_ retained|retain|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 007779|007779|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ with|with|IN|_ coverage|coverage|NN|_ and|and|CC|_ FPKM|fpkm|NN|_ measurements|measurement|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ frozen|frozen|JJ|_ acid-phenol|acid-phenol|NN|_ method|method|NN|_ described|describe|VBN|_ by|by|IN|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ -LRB-|-lrb-|-LRB-|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ ,|,|,|_ 1992|1992|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNaseI|dnasei|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ ScriptseqTM|ScriptseqTM|NNP|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ preparation|preparation|NN|_ kit|kit|NN|_ with|with|IN|_ 50|50|CD|_ ng|ng|NN|_ of|of|IN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ ;|;|:|_ Strand|Strand|NNP|_ orientated|orientate|VBD|_ RNA-Seq|rna-seq|JJ|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ nickel|nickel|NN|_ condition|condition|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ nickel|nickel|NN|_ condition|condition|NN|_
Agnès|Agnès|NNP|_ ,|,|,|_ ,|,|,|_ Rodrigue|Rodrigue|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ HCS|hcs|NN|_ 2.0.5|2.0.5|CD|_ and|and|CC|_ RTA|RTA|NNP|_ 1.17.20|1.17.20|CD|_
RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ 1.8.2|1.8.2|CD|_
Gene|Gene|NNP|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ based|base|VBN|_ on|on|IN|_ known|known|JJ|_ genes|gene|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ 2.0.2|2.0.2|CD|_ ,|,|,|_ only|only|RB|_ PF|pf|NN|_ reads|read|VBZ|_ were|be|VBD|_ retained|retain|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 007779|007779|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ with|with|IN|_ coverage|coverage|NN|_ and|and|CC|_ FPKM|fpkm|NN|_ measurements|measurement|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ frozen|frozen|JJ|_ acid-phenol|acid-phenol|NN|_ method|method|NN|_ described|describe|VBN|_ by|by|IN|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ -LRB-|-lrb-|-LRB-|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ ,|,|,|_ 1992|1992|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNaseI|dnasei|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ ScriptseqTM|ScriptseqTM|NNP|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ preparation|preparation|NN|_ kit|kit|NN|_ with|with|IN|_ 50|50|CD|_ ng|ng|NN|_ of|of|IN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ ;|;|:|_ Strand|Strand|NNP|_ orientated|orientate|VBD|_ RNA-Seq|rna-seq|JJ|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ nickel|nickel|NN|_ condition|condition|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ nickel|nickel|NN|_ condition|condition|NN|_
Agnès|Agnès|NNP|_ ,|,|,|_ ,|,|,|_ Rodrigue|Rodrigue|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ HCS|hcs|NN|_ 2.0.5|2.0.5|CD|_ and|and|CC|_ RTA|RTA|NNP|_ 1.17.20|1.17.20|CD|_
RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ 1.8.2|1.8.2|CD|_
Gene|Gene|NNP|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ based|base|VBN|_ on|on|IN|_ known|known|JJ|_ genes|gene|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ 2.0.2|2.0.2|CD|_ ,|,|,|_ only|only|RB|_ PF|pf|NN|_ reads|read|VBZ|_ were|be|VBD|_ retained|retain|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 007779|007779|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ with|with|IN|_ coverage|coverage|NN|_ and|and|CC|_ FPKM|fpkm|NN|_ measurements|measurement|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ frozen|frozen|JJ|_ acid-phenol|acid-phenol|NN|_ method|method|NN|_ described|describe|VBN|_ by|by|IN|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ -LRB-|-lrb-|-LRB-|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ ,|,|,|_ 1992|1992|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNaseI|dnasei|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ ScriptseqTM|ScriptseqTM|NNP|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ preparation|preparation|NN|_ kit|kit|NN|_ with|with|IN|_ 50|50|CD|_ ng|ng|NN|_ of|of|IN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ ;|;|:|_ Strand|Strand|NNP|_ orientated|orientate|VBD|_ RNA-Seq|rna-seq|JJ|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ nickel|nickel|NN|_ condition|condition|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ nickel|nickel|NN|_ condition|condition|NN|_
Agnès|Agnès|NNP|_ ,|,|,|_ ,|,|,|_ Rodrigue|Rodrigue|NNP|_
The|the|DT|_ program|program|NN|_ Rockhopper|rockhopper|NN|_ -LRB-|-lrb-|-LRB-|_ described|describe|VBN|_ in|in|IN|_ Mc|mc|NN|_ Clure|clure|NN|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nucleic|nucleic|JJ|_ Acids|Acids|NNP|_ Research|Research|NNP|_ .|.|.|_ 2013|2013|CD|_ ,|,|,|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Genome|Genome|NNP|_ _|_|SYM|_ builg|builg|NN|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Excel|Excel|NNP|_ formatted|format|VBD|_ matrix|matrix|NN|_ table|table|NN|_ containing|contain|VBG|_ transcript|transcript|NN|_ coordinates|coordinate|VBZ|_ ,|,|,|_ normalized|normalize|VBD|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ across|across|IN|_ the|the|DT|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ fold-changes|fold-change|VBZ|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ cells|cell|NNS|_ expressing|express|VBG|_ Vector|Vector|NNP|_ and|and|CC|_ DicF|dicf|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ xlsx|xlsx|NN|_ :|:|:|_ Excel|Excel|NNP|_ file|file|NN|_ with|with|IN|_ transcription|transcription|NN|_ start|start|NN|_ and|and|CC|_ stop|stop|VB|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ all|all|DT|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ in|in|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ raw|raw|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-operon|Processed-VectorvsDicF-operon|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ tab|tab|NN|_ delimited|delimit|VBD|_ file|file|NN|_ with|with|IN|_ operons|operon|NNS|_ expressed|express|VBN|_ differently|differently|RB|_ between|between|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ ,|,|,|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugge|Crombrugge|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p11905-11910|p11905-11910|JJ|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ mRNA-enriched|mrna-enriched|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ indexed|index|VBN|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ ™|™|CD|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ delta|delta|NN|_ dicF|dicf|NN|GEN ,|,|,|_ lacIq|laciq|NN|_
protocol|protocol|NN|_ :|:|:|_ vector|vector|NN|_ control|control|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
Carin|Carin|NNP|_ ,|,|,|_ K.|K.|NNP|_ ,|,|,|_ Vanderpool|Vanderpool|NNP|_
The|the|DT|_ program|program|NN|_ Rockhopper|rockhopper|NN|_ -LRB-|-lrb-|-LRB-|_ described|describe|VBN|_ in|in|IN|_ Mc|mc|NN|_ Clure|clure|NN|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nucleic|nucleic|JJ|_ Acids|Acids|NNP|_ Research|Research|NNP|_ .|.|.|_ 2013|2013|CD|_ ,|,|,|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Genome|Genome|NNP|_ _|_|SYM|_ builg|builg|NN|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Excel|Excel|NNP|_ formatted|format|VBD|_ matrix|matrix|NN|_ table|table|NN|_ containing|contain|VBG|_ transcript|transcript|NN|_ coordinates|coordinate|VBZ|_ ,|,|,|_ normalized|normalize|VBD|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ across|across|IN|_ the|the|DT|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ fold-changes|fold-change|VBZ|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ cells|cell|NNS|_ expressing|express|VBG|_ Vector|Vector|NNP|_ and|and|CC|_ DicF|dicf|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ xlsx|xlsx|NN|_ :|:|:|_ Excel|Excel|NNP|_ file|file|NN|_ with|with|IN|_ transcription|transcription|NN|_ start|start|NN|_ and|and|CC|_ stop|stop|VB|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ all|all|DT|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ in|in|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ raw|raw|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-operon|Processed-VectorvsDicF-operon|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ tab|tab|NN|_ delimited|delimit|VBD|_ file|file|NN|_ with|with|IN|_ operons|operon|NNS|_ expressed|express|VBN|_ differently|differently|RB|_ between|between|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ ,|,|,|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugge|Crombrugge|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p11905-11910|p11905-11910|JJ|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ mRNA-enriched|mrna-enriched|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ indexed|index|VBN|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ ™|™|CD|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ delta|delta|NN|_ dicF|dicf|NN|GEN ,|,|,|_ lacIq|laciq|NN|_
protocol|protocol|NN|_ :|:|:|_ vector|vector|NN|_ control|control|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
Carin|Carin|NNP|_ ,|,|,|_ K.|K.|NNP|_ ,|,|,|_ Vanderpool|Vanderpool|NNP|_
The|the|DT|_ program|program|NN|_ Rockhopper|rockhopper|NN|_ -LRB-|-lrb-|-LRB-|_ described|describe|VBN|_ in|in|IN|_ Mc|mc|NN|_ Clure|clure|NN|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nucleic|nucleic|JJ|_ Acids|Acids|NNP|_ Research|Research|NNP|_ .|.|.|_ 2013|2013|CD|_ ,|,|,|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Genome|Genome|NNP|_ _|_|SYM|_ builg|builg|NN|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Excel|Excel|NNP|_ formatted|format|VBD|_ matrix|matrix|NN|_ table|table|NN|_ containing|contain|VBG|_ transcript|transcript|NN|_ coordinates|coordinate|VBZ|_ ,|,|,|_ normalized|normalize|VBD|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ across|across|IN|_ the|the|DT|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ fold-changes|fold-change|VBZ|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ cells|cell|NNS|_ expressing|express|VBG|_ Vector|Vector|NNP|_ and|and|CC|_ DicF|dicf|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ xlsx|xlsx|NN|_ :|:|:|_ Excel|Excel|NNP|_ file|file|NN|_ with|with|IN|_ transcription|transcription|NN|_ start|start|NN|_ and|and|CC|_ stop|stop|VB|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ all|all|DT|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ in|in|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ raw|raw|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-operon|Processed-VectorvsDicF-operon|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ tab|tab|NN|_ delimited|delimit|VBD|_ file|file|NN|_ with|with|IN|_ operons|operon|NNS|_ expressed|express|VBN|_ differently|differently|RB|_ between|between|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ ,|,|,|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugge|Crombrugge|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p11905-11910|p11905-11910|JJ|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ mRNA-enriched|mrna-enriched|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ indexed|index|VBN|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ ™|™|CD|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ delta|delta|NN|_ dicF|dicf|NN|GEN ,|,|,|_ lacIq|laciq|NN|_
protocol|protocol|NN|_ :|:|:|_ vector|vector|NN|_ control|control|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
Carin|Carin|NNP|_ ,|,|,|_ K.|K.|NNP|_ ,|,|,|_ Vanderpool|Vanderpool|NNP|_
The|the|DT|_ program|program|NN|_ Rockhopper|rockhopper|NN|_ -LRB-|-lrb-|-LRB-|_ described|describe|VBN|_ in|in|IN|_ Mc|mc|NN|_ Clure|clure|NN|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nucleic|nucleic|JJ|_ Acids|Acids|NNP|_ Research|Research|NNP|_ .|.|.|_ 2013|2013|CD|_ ,|,|,|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Genome|Genome|NNP|_ _|_|SYM|_ builg|builg|NN|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Excel|Excel|NNP|_ formatted|format|VBD|_ matrix|matrix|NN|_ table|table|NN|_ containing|contain|VBG|_ transcript|transcript|NN|_ coordinates|coordinate|VBZ|_ ,|,|,|_ normalized|normalize|VBD|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ across|across|IN|_ the|the|DT|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ fold-changes|fold-change|VBZ|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ cells|cell|NNS|_ expressing|express|VBG|_ Vector|Vector|NNP|_ and|and|CC|_ DicF|dicf|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ xlsx|xlsx|NN|_ :|:|:|_ Excel|Excel|NNP|_ file|file|NN|_ with|with|IN|_ transcription|transcription|NN|_ start|start|NN|_ and|and|CC|_ stop|stop|VB|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ all|all|DT|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ in|in|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ raw|raw|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-operon|Processed-VectorvsDicF-operon|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ tab|tab|NN|_ delimited|delimit|VBD|_ file|file|NN|_ with|with|IN|_ operons|operon|NNS|_ expressed|express|VBN|_ differently|differently|RB|_ between|between|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ ,|,|,|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugge|Crombrugge|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p11905-11910|p11905-11910|JJ|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ mRNA-enriched|mrna-enriched|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ indexed|index|VBN|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ ™|™|CD|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ delta|delta|NN|_ dicF|dicf|NN|GEN ,|,|,|_ lacIq|laciq|NN|_
protocol|protocol|NN|_ :|:|:|_ small|small|JJ|_ RNA|rna|NN|_ DicF|dicf|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
Carin|Carin|NNP|_ ,|,|,|_ K.|K.|NNP|_ ,|,|,|_ Vanderpool|Vanderpool|NNP|_
The|the|DT|_ program|program|NN|_ Rockhopper|rockhopper|NN|_ -LRB-|-lrb-|-LRB-|_ described|describe|VBN|_ in|in|IN|_ Mc|mc|NN|_ Clure|clure|NN|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nucleic|nucleic|JJ|_ Acids|Acids|NNP|_ Research|Research|NNP|_ .|.|.|_ 2013|2013|CD|_ ,|,|,|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Genome|Genome|NNP|_ _|_|SYM|_ builg|builg|NN|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Excel|Excel|NNP|_ formatted|format|VBD|_ matrix|matrix|NN|_ table|table|NN|_ containing|contain|VBG|_ transcript|transcript|NN|_ coordinates|coordinate|VBZ|_ ,|,|,|_ normalized|normalize|VBD|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ across|across|IN|_ the|the|DT|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ fold-changes|fold-change|VBZ|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ cells|cell|NNS|_ expressing|express|VBG|_ Vector|Vector|NNP|_ and|and|CC|_ DicF|dicf|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ xlsx|xlsx|NN|_ :|:|:|_ Excel|Excel|NNP|_ file|file|NN|_ with|with|IN|_ transcription|transcription|NN|_ start|start|NN|_ and|and|CC|_ stop|stop|VB|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ all|all|DT|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ in|in|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ raw|raw|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-operon|Processed-VectorvsDicF-operon|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ tab|tab|NN|_ delimited|delimit|VBD|_ file|file|NN|_ with|with|IN|_ operons|operon|NNS|_ expressed|express|VBN|_ differently|differently|RB|_ between|between|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ ,|,|,|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugge|Crombrugge|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p11905-11910|p11905-11910|JJ|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ mRNA-enriched|mrna-enriched|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ indexed|index|VBN|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ ™|™|CD|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ delta|delta|NN|_ dicF|dicf|NN|GEN ,|,|,|_ lacIq|laciq|NN|_
protocol|protocol|NN|_ :|:|:|_ small|small|JJ|_ RNA|rna|NN|_ DicF|dicf|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
Carin|Carin|NNP|_ ,|,|,|_ K.|K.|NNP|_ ,|,|,|_ Vanderpool|Vanderpool|NNP|_
The|the|DT|_ program|program|NN|_ Rockhopper|rockhopper|NN|_ -LRB-|-lrb-|-LRB-|_ described|describe|VBN|_ in|in|IN|_ Mc|mc|NN|_ Clure|clure|NN|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nucleic|nucleic|JJ|_ Acids|Acids|NNP|_ Research|Research|NNP|_ .|.|.|_ 2013|2013|CD|_ ,|,|,|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Genome|Genome|NNP|_ _|_|SYM|_ builg|builg|NN|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ ASM584v1|asm584v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Excel|Excel|NNP|_ formatted|format|VBD|_ matrix|matrix|NN|_ table|table|NN|_ containing|contain|VBG|_ transcript|transcript|NN|_ coordinates|coordinate|VBZ|_ ,|,|,|_ normalized|normalize|VBD|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ across|across|IN|_ the|the|DT|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ fold-changes|fold-change|VBZ|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ cells|cell|NNS|_ expressing|express|VBG|_ Vector|Vector|NNP|_ and|and|CC|_ DicF|dicf|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ xlsx|xlsx|NN|_ :|:|:|_ Excel|Excel|NNP|_ file|file|NN|_ with|with|IN|_ transcription|transcription|NN|_ start|start|NN|_ and|and|CC|_ stop|stop|VB|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ all|all|DT|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ in|in|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ raw|raw|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-operon|Processed-VectorvsDicF-operon|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ tab|tab|NN|_ delimited|delimit|VBD|_ file|file|NN|_ with|with|IN|_ operons|operon|NNS|_ expressed|express|VBN|_ differently|differently|RB|_ between|between|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ ,|,|,|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugge|Crombrugge|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p11905-11910|p11905-11910|JJ|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ mRNA-enriched|mrna-enriched|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ indexed|index|VBN|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ ™|™|CD|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ delta|delta|NN|_ dicF|dicf|NN|GEN ,|,|,|_ lacIq|laciq|NN|_
protocol|protocol|NN|_ :|:|:|_ small|small|JJ|_ RNA|rna|NN|_ DicF|dicf|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug/ml|100ug/ml|JJ|_ ampicillin|ampicillin|NN|_ to|to|TO|_ retain|retain|VB|_ the|the|DT|_ plasmids|plasmid|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
Carin|Carin|NNP|_ ,|,|,|_ K.|K.|NNP|_ ,|,|,|_ Vanderpool|Vanderpool|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ were|be|VBD|_ filtered|filter|VBN|_ rapidly|rapidly|RB|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 650|650|CD|_ µL|µl|NN|_ of|of|IN|_ frozen|frozen|JJ|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 100mM|100mm|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 20mM|20mm|NN|_ Tris-HCl|tris-hcl|NN|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ Nonidet|nonidet|JJ|_ P40|p40|NN|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ ,|,|,|_ 100|100|CD|_ U/mL|u/ml|NN|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1mM|1mm|NN|_ chloramphenicol|chloramphenicol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10mL|10ml|NN|_ canisters|canister|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_ For|for|IN|_ mRNA-seq|mrna-seq|NN|_ and|and|CC|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 8000rpm|8000rpm|CD|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extracted|extract|VBN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ and|and|CC|_ small|small|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ MICROBExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ Ribozero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MEGAclear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
The|the|DT|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ fragmented|fragmented|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ miRNA|miRNA|NNP|_ cloning|clone|VBG|_ linker-1|linker-1|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ truncated|truncate|VBN|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ 2|2|CD|_ K227Q|k227q|NN|_ .|.|.|_ The|the|DT|_ ligated|ligate|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ reverse|reverse|JJ|_ transribed|transribe|VBN|_ using|use|VBG|_ the|the|DT|_ primer|primer|NN|_ 5Phos/GATCGTCGGACTGTAGAACTCTGAACCTGTCGGTGGTCGCC|5phos/gatcgtcggactgtagaactctgaacctgtcggtggtcgcc|NN|_ GTATCATT/iSp18/CACTCA|gtatcatt/isp18/cactca|NN|_ /|/|:|_ iSp18/CAAGCAGAAGACGGCATACGAATTGATG|isp18/caagcagaagacggcatacgaattgatg|NN|_ GTGCCTACAG|gtgcctacag|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ with|with|IN|_ CircLigase|circligase|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ PCR|pcr|NN|_ amplification|amplification|NN|_ was|be|VBD|_ done|do|VBN|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Ingolia|Ingolia|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ full|full|JJ|_ supplement|supplement|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ minus|minus|CC|_ methionine|methionine|NN|SUPP .|.|.|_ An|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 400-fold|400-fold|JJ|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ a|a|DT|_ 1|1|CD|_ liter|liter|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ aeration|aeration|NN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ kasugamycin|kasugamycin|NN|_ -LRB-|-lrb-|-LRB-|_ ksg|ksg|NN|_ -RRB-|-rrb-|-RRB-|_ experiments|experiment|NNS|_ ,|,|,|_ ksg|ksg|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 10|10|CD|_ mg/mL|mg/ml|NN|_ to|to|TO|_ ΔgcvB|δgcvb|NN|_ cells|cell|NNS|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ DMS|DMS|NNP|_ modification|modification|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ in|in|FW|_ vitro|vitro|FW|_ DMS|dms|NN|_ modifications|modification|NNS|_ ,|,|,|_ mRNA|mrna|NN|_ was|be|VBD|_ denatured|denature|VBN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ cooled|cool|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ refolded|refold|VBN|_ in|in|IN|_ 90|90|CD|_ µL|µl|NN|_ RNA|rna|NN|_ folding|folding|JJ|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 6|6|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ then|then|RB|_ incubated|incubate|VBN|_ in|in|IN|_ either|either|CC|_ .2|.2|NN|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 4|4|CD|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ -LSB-|-lsb-|-LRB-|_ p-CTRL|p-ctrl|NN|_ -RSB-|-rsb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_
All|all|DT|_ cultures|culture|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ full|full|JJ|_ supplement|supplement|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ minus|minus|CC|_ methionine|methionine|NN|SUPP .|.|.|_ An|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 400-fold|400-fold|JJ|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ a|a|DT|_ 1|1|CD|_ liter|liter|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ aeration|aeration|NN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ kasugamycin|kasugamycin|NN|_ -LRB-|-lrb-|-LRB-|_ ksg|ksg|NN|_ -RRB-|-rrb-|-RRB-|_ experiments|experiment|NNS|_ ,|,|,|_ ksg|ksg|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 10|10|CD|_ mg/mL|mg/ml|NN|_ to|to|TO|_ ΔgcvB|δgcvb|NN|_ cells|cell|NNS|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ DMS|DMS|NNP|_ modification|modification|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ in|in|FW|_ vitro|vitro|FW|_ DMS|dms|NN|_ modifications|modification|NNS|_ ,|,|,|_ mRNA|mrna|NN|_ was|be|VBD|_ denatured|denature|VBN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ cooled|cool|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ refolded|refold|VBN|_ in|in|IN|_ 90|90|CD|_ µL|µl|NN|_ RNA|rna|NN|_ folding|folding|JJ|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 6|6|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ then|then|RB|_ incubated|incubate|VBN|_ in|in|IN|_ either|either|CC|_ .2|.2|NN|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 4|4|CD|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ were|be|VBD|_ filtered|filter|VBN|_ rapidly|rapidly|RB|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 650|650|CD|_ µL|µl|NN|_ of|of|IN|_ frozen|frozen|JJ|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 100mM|100mm|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 20mM|20mm|NN|_ Tris-HCl|tris-hcl|NN|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ Nonidet|nonidet|JJ|_ P40|p40|NN|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ ,|,|,|_ 100|100|CD|_ U/mL|u/ml|NN|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1mM|1mm|NN|_ chloramphenicol|chloramphenicol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10mL|10ml|NN|_ canisters|canister|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_ For|for|IN|_ mRNA-seq|mrna-seq|NN|_ and|and|CC|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 8000rpm|8000rpm|CD|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extracted|extract|VBN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ and|and|CC|_ small|small|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ MICROBExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ Ribozero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MEGAclear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
The|the|DT|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ fragmented|fragmented|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ miRNA|miRNA|NNP|_ cloning|clone|VBG|_ linker-1|linker-1|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ truncated|truncate|VBN|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ 2|2|CD|_ K227Q|k227q|NN|_ .|.|.|_ The|the|DT|_ ligated|ligate|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ reverse|reverse|JJ|_ transribed|transribe|VBN|_ using|use|VBG|_ the|the|DT|_ primer|primer|NN|_ 5Phos/GATCGTCGGACTGTAGAACTCTGAACCTGTCGGTGGTCGCC|5phos/gatcgtcggactgtagaactctgaacctgtcggtggtcgcc|NN|_ GTATCATT/iSp18/CACTCA|gtatcatt/isp18/cactca|NN|_ /|/|:|_ iSp18/CAAGCAGAAGACGGCATACGAATTGATG|isp18/caagcagaagacggcatacgaattgatg|NN|_ GTGCCTACAG|gtgcctacag|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ with|with|IN|_ CircLigase|circligase|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ PCR|pcr|NN|_ amplification|amplification|NN|_ was|be|VBD|_ done|do|VBN|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Ingolia|Ingolia|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ full|full|JJ|_ supplement|supplement|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ minus|minus|CC|_ methionine|methionine|NN|SUPP .|.|.|_ An|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 400-fold|400-fold|JJ|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ a|a|DT|_ 1|1|CD|_ liter|liter|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ aeration|aeration|NN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ kasugamycin|kasugamycin|NN|_ -LRB-|-lrb-|-LRB-|_ ksg|ksg|NN|_ -RRB-|-rrb-|-RRB-|_ experiments|experiment|NNS|_ ,|,|,|_ ksg|ksg|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 10|10|CD|_ mg/mL|mg/ml|NN|_ to|to|TO|_ ΔgcvB|δgcvb|NN|_ cells|cell|NNS|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ DMS|DMS|NNP|_ modification|modification|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ in|in|FW|_ vitro|vitro|FW|_ DMS|dms|NN|_ modifications|modification|NNS|_ ,|,|,|_ mRNA|mrna|NN|_ was|be|VBD|_ denatured|denature|VBN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ cooled|cool|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ refolded|refold|VBN|_ in|in|IN|_ 90|90|CD|_ µL|µl|NN|_ RNA|rna|NN|_ folding|folding|JJ|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 6|6|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ then|then|RB|_ incubated|incubate|VBN|_ in|in|IN|_ either|either|CC|_ .2|.2|NN|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 4|4|CD|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ -LSB-|-lsb-|-LRB-|_ p-CUA|p-cua|NN|_ -RSB-|-rsb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_
All|all|DT|_ cultures|culture|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ full|full|JJ|_ supplement|supplement|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ minus|minus|CC|_ methionine|methionine|NN|SUPP .|.|.|_ An|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 400-fold|400-fold|JJ|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ a|a|DT|_ 1|1|CD|_ liter|liter|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ aeration|aeration|NN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ kasugamycin|kasugamycin|NN|_ -LRB-|-lrb-|-LRB-|_ ksg|ksg|NN|_ -RRB-|-rrb-|-RRB-|_ experiments|experiment|NNS|_ ,|,|,|_ ksg|ksg|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 10|10|CD|_ mg/mL|mg/ml|NN|_ to|to|TO|_ ΔgcvB|δgcvb|NN|_ cells|cell|NNS|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ DMS|DMS|NNP|_ modification|modification|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ in|in|FW|_ vitro|vitro|FW|_ DMS|dms|NN|_ modifications|modification|NNS|_ ,|,|,|_ mRNA|mrna|NN|_ was|be|VBD|_ denatured|denature|VBN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ cooled|cool|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ refolded|refold|VBN|_ in|in|IN|_ 90|90|CD|_ µL|µl|NN|_ RNA|rna|NN|_ folding|folding|JJ|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 6|6|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ then|then|RB|_ incubated|incubate|VBN|_ in|in|IN|_ either|either|CC|_ .2|.2|NN|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 4|4|CD|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ were|be|VBD|_ filtered|filter|VBN|_ rapidly|rapidly|RB|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 650|650|CD|_ µL|µl|NN|_ of|of|IN|_ frozen|frozen|JJ|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 100mM|100mm|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 20mM|20mm|NN|_ Tris-HCl|tris-hcl|NN|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ Nonidet|nonidet|JJ|_ P40|p40|NN|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ ,|,|,|_ 100|100|CD|_ U/mL|u/ml|NN|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1mM|1mm|NN|_ chloramphenicol|chloramphenicol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10mL|10ml|NN|_ canisters|canister|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_ For|for|IN|_ mRNA-seq|mrna-seq|NN|_ and|and|CC|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 8000rpm|8000rpm|CD|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extracted|extract|VBN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ and|and|CC|_ small|small|JJ|_ RNA|rna|NN|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ MICROBExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ Ribozero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MEGAclear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
The|the|DT|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ fragmented|fragmented|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ miRNA|miRNA|NNP|_ cloning|clone|VBG|_ linker-1|linker-1|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ truncated|truncate|VBN|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ 2|2|CD|_ K227Q|k227q|NN|_ .|.|.|_ The|the|DT|_ ligated|ligate|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ reverse|reverse|JJ|_ transribed|transribe|VBN|_ using|use|VBG|_ the|the|DT|_ primer|primer|NN|_ 5Phos/GATCGTCGGACTGTAGAACTCTGAACCTGTCGGTGGTCGCC|5phos/gatcgtcggactgtagaactctgaacctgtcggtggtcgcc|NN|_ GTATCATT/iSp18/CACTCA|gtatcatt/isp18/cactca|NN|_ /|/|:|_ iSp18/CAAGCAGAAGACGGCATACGAATTGATG|isp18/caagcagaagacggcatacgaattgatg|NN|_ GTGCCTACAG|gtgcctacag|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ with|with|IN|_ CircLigase|circligase|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ PCR|pcr|NN|_ amplification|amplification|NN|_ was|be|VBD|_ done|do|VBN|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Ingolia|Ingolia|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ full|full|JJ|_ supplement|supplement|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ minus|minus|CC|_ methionine|methionine|NN|SUPP .|.|.|_ An|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 400-fold|400-fold|JJ|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ a|a|DT|_ 1|1|CD|_ liter|liter|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ aeration|aeration|NN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ kasugamycin|kasugamycin|NN|_ -LRB-|-lrb-|-LRB-|_ ksg|ksg|NN|_ -RRB-|-rrb-|-RRB-|_ experiments|experiment|NNS|_ ,|,|,|_ ksg|ksg|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 10|10|CD|_ mg/mL|mg/ml|NN|_ to|to|TO|_ ΔgcvB|δgcvb|NN|_ cells|cell|NNS|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ DMS|DMS|NNP|_ modification|modification|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ in|in|FW|_ vitro|vitro|FW|_ DMS|dms|NN|_ modifications|modification|NNS|_ ,|,|,|_ mRNA|mrna|NN|_ was|be|VBD|_ denatured|denature|VBN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ cooled|cool|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ refolded|refold|VBN|_ in|in|IN|_ 90|90|CD|_ µL|µl|NN|_ RNA|rna|NN|_ folding|folding|JJ|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 6|6|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ then|then|RB|_ incubated|incubate|VBN|_ in|in|IN|_ either|either|CC|_ .2|.2|NN|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 4|4|CD|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ -LSB-|-lsb-|-LRB-|_ p-CUG|p-cug|NN|_ -RSB-|-rsb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_
All|all|DT|_ cultures|culture|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ full|full|JJ|_ supplement|supplement|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ minus|minus|CC|_ methionine|methionine|NN|SUPP .|.|.|_ An|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 400-fold|400-fold|JJ|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ a|a|DT|_ 1|1|CD|_ liter|liter|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ aeration|aeration|NN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacteria|bacterium|NNS|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ kasugamycin|kasugamycin|NN|_ -LRB-|-lrb-|-LRB-|_ ksg|ksg|NN|_ -RRB-|-rrb-|-RRB-|_ experiments|experiment|NNS|_ ,|,|,|_ ksg|ksg|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 10|10|CD|_ mg/mL|mg/ml|NN|_ to|to|TO|_ ΔgcvB|δgcvb|NN|_ cells|cell|NNS|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ DMS|DMS|NNP|_ modification|modification|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ in|in|FW|_ vitro|vitro|FW|_ DMS|dms|NN|_ modifications|modification|NNS|_ ,|,|,|_ mRNA|mrna|NN|_ was|be|VBD|_ denatured|denature|VBN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ cooled|cool|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ refolded|refold|VBN|_ in|in|IN|_ 90|90|CD|_ µL|µl|NN|_ RNA|rna|NN|_ folding|folding|JJ|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 6|6|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ then|then|RB|_ incubated|incubate|VBN|_ in|in|IN|_ either|either|CC|_ .2|.2|NN|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 4|4|CD|_ %|%|NN|_ DMS|dms|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Yan|Yan|NNP|_ ,|,|,|_ ,|,|,|_ Zhang|Zhang|NNP|_
FastQ|FastQ|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_ FastX|fastx|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ -RRB-|-rrb-|-RRB-|_
5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ linker|linker|NN|_ and|and|CC|_ poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
mapping|mapping|NN|_ of|of|IN|_ non-rRNA|non-rrna|JJ|_ and|and|CC|_ tRNA|trna|NN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ chromosome|chromosome|NN|_ and|and|CC|_ plasmids|plasmid|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
generation|generation|NN|_ of|of|IN|_ coverage|coverage|NN|_ graphs|graph|NNS|_ representing|represent|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ pAA|paa|NN|_ plasmid-associated|plasmid-associated|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_
normalization|normalization|NN|_ of|of|IN|_ graphs|graph|NNS|_ to|to|TO|_ the|the|DT|_ total|total|JJ|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ library|library|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 018658.1|018658.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018659.1|018659.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018660.1|018660.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018666.1|018666.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wig|wig|NN|_ files|file|NNS|_ representing|represent|VBG|_ the|the|DT|_ normalized|normalize|VBN|_ number|number|NN|_ of|of|IN|_ pAA-associated|paa-associated|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ .|.|.|_ Files|file|NNS|_ contain|contain|VBP|_ wiggle-formatted|wiggle-formatted|JJ|_ files|file|NNS|_ data|datum|NNS|_ for|for|IN|_ accessions|accession|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018659.1|018659.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018660.1|018660.1|CD|_ ,|,|,|_ and|and|CC|_ NC|NC|NNP|_ _|_|SYM|_ 018666.1|018666.1|CD|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 1U|1u|NN|_ /|/|:|_ L|l|NN|_ RiboLock|ribolock|NN|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ the|the|DT|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ TEX|tex|NN|_ +|+|CC|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ processed|process|VBN|_ RNAs|rna|NNS|_ using|use|VBG|_ 1U|1u|NN|_ per|per|IN|_ 1μg|1μg|NN|_ of|of|IN|_ RNA|rna|NN|_ Terminator|Terminator|NNP|_ 5|5|CD|_ '|'|''|_ -|-|:|_ Phosphate-Dependent|phosphate-dependent|JJ|_ Exonuclease|exonuclease|NN|_ -LRB-|-lrb-|-LRB-|_ TEX|tex|NN|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 1U/μL|1u/μl|NN|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 30|30|CD|_ °|°|CD|_ C|c|NN|_ .|.|.|_ A|a|DT|_ control|control|NN|_ reaction|reaction|NN|_ without|without|IN|_ TEX|TEX|NNP|_ -LRB-|-lrb-|-LRB-|_ TEX|TEX|NNP|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ run|run|VBN|_ in|in|IN|_ parallel|parallel|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNase-free|rnase-free|JJ|_ water|water|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnology|Biotechnology|NNP|_ AG|AG|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Berezikov|Berezikov|NNP|_ et|et|FW|_ al.|al.|FW|_ ,2006|,2006|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ without|without|IN|_ the|the|DT|_ RNA|rna|NN|_ size-fractionation|size-fractionation|NN|_ step|step|NN|_ prior|prior|RB|_ to|to|TO|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ polyA-tailed|polya-tailed|JJ|_ using|use|VBG|_ polyA|polya|NN|_ polymerase|polymerase|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ termini|terminus|NNS|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ P|p|NN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ allow|allow|VB|_ for|for|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ RNA|rna|NN|_ adapter|adapter|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ by|by|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ In|in|IN|_ a|a|DT|_ PCR-based|pcr-based|JJ|_ amplification|amplification|NN|_ step|step|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ the|the|DT|_ cDNA|cdna|NN|_ concentration|concentration|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 20-30|20-30|CD|_ ng/µl|ng/µl|NN|_ .|.|.|_ A|a|DT|_ library-specific|library-specific|JJ|_ barcode|barcode|NN|_ for|for|IN|_ multiplex|multiplex|JJ|_ sequencing|sequencing|NN|_ was|be|VBD|_ part|part|NN|_ of|of|IN|_ a|a|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ sequencing|sequencing|NN|_ adapter|adapter|NN|_ .|.|.|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ strain|strain|NN|_ LB226692|lb226692|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:10,000|1:10,000|CD|_ in|in|IN|_ pre-warmed|pre-warmed|JJ|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ for|for|IN|_ 3.5|3.5|CD|_ h|h|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.52|0.52|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O104|o104|NN|_ :|:|:|_ H4|h4|NN|_
exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ suspension|suspension|NN|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ 0.625|0.625|CD|_ ml|ml|NN|_ of|of|IN|_ pre-chilled|pre-chilled|JJ|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortexed|JJ|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ on|on|IN|_ ice|ice|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 5000|5000|CD|_ g|g|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ a|a|DT|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ bath|bath|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ oC|oc|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ clinical|clinical|JJ|_ isolate|isolate|JJ|_ LB226692|lb226692|NN|_
origin|origin|NN|_ of|of|IN|_ isolation|isolation|NN|_ :|:|:|_ patient|patient|NN|_ with|with|IN|_ hemolytic|hemolytic|JJ|_ uremic|uremic|JJ|_ syndrome|syndrome|NN|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NN|_ -RRB-|-rrb-|-RRB-|_
outbreak|outbreak|NN|_ :|:|:|_ 2011|2011|CD|_ outbreak|outbreak|NN|_ centered|center|VBN|_ in|in|IN|_ Northern|Northern|NNP|_ Germany|Germany|NNP|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ strain|strain|NN|_ LB226692|lb226692|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:10,000|1:10,000|CD|_ in|in|IN|_ pre-warmed|pre-warmed|JJ|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ for|for|IN|_ 3.5|3.5|CD|_ h|h|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.52|0.52|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O104|o104|NN|_ :|:|:|_ H4|h4|NN|_
exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ suspension|suspension|NN|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ 0.625|0.625|CD|_ ml|ml|NN|_ of|of|IN|_ pre-chilled|pre-chilled|JJ|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortexed|JJ|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ on|on|IN|_ ice|ice|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 5000|5000|CD|_ g|g|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ a|a|DT|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ bath|bath|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ oC|oc|NN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
FastQ|FastQ|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_ FastX|fastx|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ -RRB-|-rrb-|-RRB-|_
5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ linker|linker|NN|_ and|and|CC|_ poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
mapping|mapping|NN|_ of|of|IN|_ non-rRNA|non-rrna|JJ|_ and|and|CC|_ tRNA|trna|NN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ chromosome|chromosome|NN|_ and|and|CC|_ plasmids|plasmid|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
generation|generation|NN|_ of|of|IN|_ coverage|coverage|NN|_ graphs|graph|NNS|_ representing|represent|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ pAA|paa|NN|_ plasmid-associated|plasmid-associated|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_
normalization|normalization|NN|_ of|of|IN|_ graphs|graph|NNS|_ to|to|TO|_ the|the|DT|_ total|total|JJ|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ library|library|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 018658.1|018658.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018659.1|018659.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018660.1|018660.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018666.1|018666.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wig|wig|NN|_ files|file|NNS|_ representing|represent|VBG|_ the|the|DT|_ normalized|normalize|VBN|_ number|number|NN|_ of|of|IN|_ pAA-associated|paa-associated|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ .|.|.|_ Files|file|NNS|_ contain|contain|VBP|_ wiggle-formatted|wiggle-formatted|JJ|_ files|file|NNS|_ data|datum|NNS|_ for|for|IN|_ accessions|accession|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018659.1|018659.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018660.1|018660.1|CD|_ ,|,|,|_ and|and|CC|_ NC|NC|NNP|_ _|_|SYM|_ 018666.1|018666.1|CD|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 1U|1u|NN|_ /|/|:|_ L|l|NN|_ RiboLock|ribolock|NN|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ -LRB-|-lrb-|-LRB-|_ 1x|1x|NN|_ 25:24:1|25:24:1|CD|_ v/v|v/v|NN|_ phenol/chloroform|phenol/chloroform|NN|_ /|/|:|_ isoamyalcohol|isoamyalcohol|NN|_ ,|,|,|_ 1x|1x|NN|_ chloroform|chloroform|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ with|with|IN|_ 3|3|CD|_ volumes|volume|NNS|_ of|of|IN|_ 30:1|30:1|CD|_ 100|100|CD|_ %|%|NN|_ ethanol/3|ethanol/3|CD|_ M|m|NN|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ the|the|DT|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ TEX|tex|NN|_ +|+|CC|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ processed|process|VBN|_ RNAs|rna|NNS|_ using|use|VBG|_ 1U|1u|NN|_ per|per|IN|_ 1μg|1μg|NN|_ of|of|IN|_ RNA|rna|NN|_ Terminator|Terminator|NNP|_ 5|5|CD|_ '|'|''|_ -|-|:|_ Phosphate-Dependent|phosphate-dependent|JJ|_ Exonuclease|exonuclease|NN|_ -LRB-|-lrb-|-LRB-|_ TEX|tex|NN|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 1U/μL|1u/μl|NN|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_ at|at|IN|_ 30|30|CD|_ °|°|CD|_ C|c|NN|_ .|.|.|_ A|a|DT|_ control|control|NN|_ reaction|reaction|NN|_ without|without|IN|_ TEX|TEX|NNP|_ -LRB-|-lrb-|-LRB-|_ TEX|TEX|NNP|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ run|run|VBN|_ in|in|IN|_ parallel|parallel|NN|_ .|.|.|_ Following|follow|VBG|_ organic|organic|JJ|_ extraction|extraction|NN|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ overnight|overnight|JJ|_ precipitation|precipitation|NN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNase-free|rnase-free|JJ|_ water|water|NN|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnology|Biotechnology|NNP|_ AG|AG|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Berezikov|Berezikov|NNP|_ et|et|FW|_ al.|al.|FW|_ ,2006|,2006|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ without|without|IN|_ the|the|DT|_ RNA|rna|NN|_ size-fractionation|size-fractionation|NN|_ step|step|NN|_ prior|prior|RB|_ to|to|TO|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ polyA-tailed|polya-tailed|JJ|_ using|use|VBG|_ polyA|polya|NN|_ polymerase|polymerase|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ PPP|ppp|NN|_ termini|terminus|NNS|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ P|p|NN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ allow|allow|VB|_ for|for|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ RNA|rna|NN|_ adapter|adapter|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ by|by|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ In|in|IN|_ a|a|DT|_ PCR-based|pcr-based|JJ|_ amplification|amplification|NN|_ step|step|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ the|the|DT|_ cDNA|cdna|NN|_ concentration|concentration|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 20-30|20-30|CD|_ ng/µl|ng/µl|NN|_ .|.|.|_ A|a|DT|_ library-specific|library-specific|JJ|_ barcode|barcode|NN|_ for|for|IN|_ multiplex|multiplex|JJ|_ sequencing|sequencing|NN|_ was|be|VBD|_ part|part|NN|_ of|of|IN|_ a|a|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ sequencing|sequencing|NN|_ adapter|adapter|NN|_ .|.|.|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ strain|strain|NN|_ LB226692|lb226692|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:10,000|1:10,000|CD|_ in|in|IN|_ pre-warmed|pre-warmed|JJ|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ for|for|IN|_ 3.5|3.5|CD|_ h|h|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.52|0.52|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O104|o104|NN|_ :|:|:|_ H4|h4|NN|_
exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ suspension|suspension|NN|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ 0.625|0.625|CD|_ ml|ml|NN|_ of|of|IN|_ pre-chilled|pre-chilled|JJ|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortexed|JJ|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ on|on|IN|_ ice|ice|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 5000|5000|CD|_ g|g|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ a|a|DT|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ bath|bath|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ oC|oc|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ clinical|clinical|JJ|_ isolate|isolate|JJ|_ LB226692|lb226692|NN|_
origin|origin|NN|_ of|of|IN|_ isolation|isolation|NN|_ :|:|:|_ patient|patient|NN|_ with|with|IN|_ hemolytic|hemolytic|JJ|_ uremic|uremic|JJ|_ syndrome|syndrome|NN|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NN|_ -RRB-|-rrb-|-RRB-|_
outbreak|outbreak|NN|_ :|:|:|_ 2011|2011|CD|_ outbreak|outbreak|NN|_ centered|center|VBN|_ in|in|IN|_ Northern|Northern|NNP|_ Germany|Germany|NNP|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ strain|strain|NN|_ LB226692|lb226692|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:10,000|1:10,000|CD|_ in|in|IN|_ pre-warmed|pre-warmed|JJ|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g/L|g/l|NN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 5|5|CD|_ g/L|g/l|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ for|for|IN|_ 3.5|3.5|CD|_ h|h|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.52|0.52|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O104|o104|NN|_ :|:|:|_ H4|h4|NN|_
exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ suspension|suspension|NN|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ 0.625|0.625|CD|_ ml|ml|NN|_ of|of|IN|_ pre-chilled|pre-chilled|JJ|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol/95|phenol/95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortexed|JJ|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ on|on|IN|_ ice|ice|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 5000|5000|CD|_ g|g|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ a|a|DT|_ dry|dry|JJ|_ ice-ethanol|ice-ethanol|NN|_ bath|bath|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ oC|oc|NN|_ .|.|.|_
Konrad|Konrad|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Förstner|Förstner|NNP|_
Gene|Gene|NNP|_ expression|expression|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ per|per|IN|_ strain|strain|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ the|the|DT|_ statistical|statistical|JJ|_ software|software|NN|_ program|program|NN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ www.r-project.org|www.r-project.org|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ EdgeR|edger|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ CQN|cqn|NN|_ package|package|NN|_ ,|,|,|_ which|which|WDT|_ accounts|account|VBZ|_ for|for|IN|_ both|both|DT|_ gene|gene|NN|_ length|length|NN|_ and|and|CC|_ GC|gc|NN|_ content|content|JJ|_ effects|effect|NNS|_ -LRB-|-lrb-|-LRB-|_ 4|4|LS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ were|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ comparing|compare|VBG|_ expression|expression|NN|_ values|value|NNS|_ under|under|IN|_ anaerobic|anaerobic|JJ|_ and|and|CC|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ .|.|.|_ Those|those|DT|_ genes|gene|NNS|_ with|with|IN|_ adjusted|adjusted|JJ|_ P|p|NN|_ values|value|NNS|_ less|less|JJR|_ than|than|IN|_ 0.01|0.01|CD|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ ,|,|,|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ less|less|JJR|_ than|than|IN|_ 1|1|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ identified|identify|VBN|_ as|as|IN|_ significantly|significantly|RB|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ gene|gene|NN|_ annotations|annotation|NNS|_ were|be|VBD|_ automatically|automatically|RB|_ made|make|VBN|_ using|use|VBG|_ the|the|DT|_ biomaRt|biomart|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ -RRB-|-rrb-|-RRB-|_ together|together|RB|_ with|with|IN|_ the|the|DT|_ annotation|annotation|NN|_ files|file|VBZ|_ available|available|JJ|_ at|at|IN|_ the|the|DT|_ Ensembl|ensembl|NN|_ database|database|NN|_ -LRB-|-lrb-|-LRB-|_ www.ensembl.org|www.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ gene|gene|NN|_ set|set|NN|_ enrichment|enrichment|NN|_ analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ GSEA|gsea|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ piano|piano|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ R|r|NN|_ packages|package|NNS|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ are|be|VBP|_ available|available|JJ|_ in|in|IN|_ Bioconductor|Bioconductor|NNP|_ -LRB-|-lrb-|-LRB-|_ www.bioconductor.org|www.bioconductor.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ gene|gene|NN|_ expresion|expresion|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ from|from|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ of|of|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.6|0.6|CD|_ -LRB-|-lrb-|-LRB-|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 10|10|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ and|and|CC|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ STOP|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.7|4.7|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 20|20|CD|_ min|min|NN|_ incubation|incubation|NN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ and|and|CC|_ 7000|7000|CD|_ x|x|CC|_ g|g|NN|_ in|in|IN|_ a|a|DT|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ from|from|IN|_ one|one|CD|_ aliquot|aliquot|NN|_ were|be|VBD|_ gently|gently|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAProtect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ further|further|JJ|_ stabilize|stabilize|VB|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ Remaining|remain|VBG|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ placed|place|VBN|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ for|for|IN|_ archival|archival|JJ|_ storage|storage|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ on|on|IN|_ column|column|NN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ '|'|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ 23S|23s|NN|_ and|and|CC|_ 16S|16s|NN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ subtractive|subtractive|JJ|_ hybridization|hybridization|NN|_ using|use|VBG|_ the|the|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ modifications|modification|NNS|_ .|.|.|_ Compared|compare|VBN|_ with|with|IN|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ ,|,|,|_ 50|50|CD|_ %|%|NN|_ more|more|JJR|_ capture|capture|NN|_ oligonucleotides|oligonucleotide|NNS|_ and|and|CC|_ magnetic|magnetic|JJ|_ beads|bead|NNS|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ 5S|5s|NN|_ rRNAs|rrna|NNS|_ -LRB-|-lrb-|-LRB-|_ 120|120|CD|_ nt|nt|NNS|_ in|in|IN|_ length|length|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ during|during|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ on|on|IN|_ column|column|NN|_ .|.|.|_ Specifically|specifically|RB|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ depletion|depletion|NN|_ on|on|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ -LRB-|-lrb-|-LRB-|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ triplicate|triplicate|NN|_ to|to|TO|_ an|a|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ .|.|.|_ RT-PCR|rt-pcr|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ SuperScript|SuperScript|NNP|_ ®|®|NNP|_ II|II|NNP|_ One-step|one-step|JJ|_ RT-PCR|rt-pcr|NN|_ reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq2000|hiseq2000|NN|_ platform|platform|NN|_ with|with|IN|_ a|a|DT|_ paired-end|paired-end|NN|_ protocol|protocol|NN|_ and|and|CC|_ read|read|VB|_ lengths|length|NNS|_ of|of|IN|_ 50|50|CD|_ nt|nt|NNS|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ measured|measure|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Fluorometer|Fluorometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ removal|removal|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ and|and|CC|_ cDNA|cdna|NN|_ library|library|NN|_ validation|validation|NN|_ were|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strains|strain|NNS|_ E.coli|e.coli|JJ|_ C|c|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 4860|4860|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ Crooks|crook|NNS|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 1576|1576|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DH5α|dh5α|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 6897|6897|CD|_ -RRB-|-rrb-|-RRB-|_ E.|e.|FW|_ coli|coli|FW|_ W|w|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 1116|1116|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 5911|5911|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ DSMZ-German|DSMZ-German|NNP|_ Collection|Collection|NNP|_ of|of|IN|_ Microorganism|Microorganism|NNP|_ and|and|CC|_ Cell|cell|NN|_ Cultures|culture|NNS|_ ;|;|:|_ E.|e.|FW|_ coli|coli|FW|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ purchased|purchase|VBN|_ as|as|IN|_ competent|competent|JJ|_ cells|cell|NNS|_ from|from|IN|_ Agilent|Agilent|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ ATCC|atcc|NN|_ 700926|700926|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ Na2HPO4|na2hpo4|NN|_ x|x|NN|_ 7H2O|7h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 6.8|6.8|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ KH2PO4|kh2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NH4Cl|nh4cl|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ mmol|mmol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mmol|mmol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ trace|trace|NN|_ elements|element|NNS|_ ,|,|,|_ Wolf|Wolf|NNP|_ 's|'s|POS|_ vitamin|vitamin|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_ L-1|l-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Anoxic|anoxic|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP was|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ flushing|flush|VBG|_ solution|solution|NN|_ with|with|IN|_ oxygen|oxygen|NN|_ free|free|JJ|_ nitrogen|nitrogen|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ of|of|IN|_ each|each|DT|_ of|of|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ optical|optical|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ or|or|CC|_ 300|300|CD|_ ml|ml|NN|_ oxygen-free|oxygen-free|JJ|_ sealed|sealed|JJ|_ bottles|bottle|NNS|_ containing|contain|VBG|_ 50|50|CD|_ ml|ml|NN|_ glucose-M9|glucose-m9|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Crooks|crook|NNS|_ _|_|VBP|_ aero|aero|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crooks|crook|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strains|strain|NNS|_ E.coli|e.coli|JJ|_ C|c|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 4860|4860|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ Crooks|crook|NNS|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 1576|1576|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DH5α|dh5α|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 6897|6897|CD|_ -RRB-|-rrb-|-RRB-|_ E.|e.|FW|_ coli|coli|FW|_ W|w|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 1116|1116|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 5911|5911|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ DSMZ-German|DSMZ-German|NNP|_ Collection|Collection|NNP|_ of|of|IN|_ Microorganism|Microorganism|NNP|_ and|and|CC|_ Cell|cell|NN|_ Cultures|culture|NNS|_ ;|;|:|_ E.|e.|FW|_ coli|coli|FW|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ purchased|purchase|VBN|_ as|as|IN|_ competent|competent|JJ|_ cells|cell|NNS|_ from|from|IN|_ Agilent|Agilent|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ ATCC|atcc|NN|_ 700926|700926|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ Na2HPO4|na2hpo4|NN|_ x|x|NN|_ 7H2O|7h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 6.8|6.8|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ KH2PO4|kh2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NH4Cl|nh4cl|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ mmol|mmol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mmol|mmol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ trace|trace|NN|_ elements|element|NNS|_ ,|,|,|_ Wolf|Wolf|NNP|_ 's|'s|POS|_ vitamin|vitamin|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_ L-1|l-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Anoxic|anoxic|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP was|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ flushing|flush|VBG|_ solution|solution|NN|_ with|with|IN|_ oxygen|oxygen|NN|_ free|free|JJ|_ nitrogen|nitrogen|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ of|of|IN|_ each|each|DT|_ of|of|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ optical|optical|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ or|or|CC|_ 300|300|CD|_ ml|ml|NN|_ oxygen-free|oxygen-free|JJ|_ sealed|sealed|JJ|_ bottles|bottle|NNS|_ containing|contain|VBG|_ 50|50|CD|_ ml|ml|NN|_ glucose-M9|glucose-m9|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Crooks|crook|NNS|_ _|_|VBP|_ aero|aero|NN|_
Jonathan|Jonathan|NNP|_ ,|,|,|_ ,|,|,|_ Monk|Monk|NNP|_
Gene|Gene|NNP|_ expression|expression|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ per|per|IN|_ strain|strain|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ the|the|DT|_ statistical|statistical|JJ|_ software|software|NN|_ program|program|NN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ www.r-project.org|www.r-project.org|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ EdgeR|edger|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ CQN|cqn|NN|_ package|package|NN|_ ,|,|,|_ which|which|WDT|_ accounts|account|VBZ|_ for|for|IN|_ both|both|DT|_ gene|gene|NN|_ length|length|NN|_ and|and|CC|_ GC|gc|NN|_ content|content|JJ|_ effects|effect|NNS|_ -LRB-|-lrb-|-LRB-|_ 4|4|LS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ were|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ comparing|compare|VBG|_ expression|expression|NN|_ values|value|NNS|_ under|under|IN|_ anaerobic|anaerobic|JJ|_ and|and|CC|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ .|.|.|_ Those|those|DT|_ genes|gene|NNS|_ with|with|IN|_ adjusted|adjusted|JJ|_ P|p|NN|_ values|value|NNS|_ less|less|JJR|_ than|than|IN|_ 0.01|0.01|CD|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ ,|,|,|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ less|less|JJR|_ than|than|IN|_ 1|1|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ identified|identify|VBN|_ as|as|IN|_ significantly|significantly|RB|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ gene|gene|NN|_ annotations|annotation|NNS|_ were|be|VBD|_ automatically|automatically|RB|_ made|make|VBN|_ using|use|VBG|_ the|the|DT|_ biomaRt|biomart|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ -RRB-|-rrb-|-RRB-|_ together|together|RB|_ with|with|IN|_ the|the|DT|_ annotation|annotation|NN|_ files|file|VBZ|_ available|available|JJ|_ at|at|IN|_ the|the|DT|_ Ensembl|ensembl|NN|_ database|database|NN|_ -LRB-|-lrb-|-LRB-|_ www.ensembl.org|www.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ gene|gene|NN|_ set|set|NN|_ enrichment|enrichment|NN|_ analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ GSEA|gsea|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ piano|piano|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ R|r|NN|_ packages|package|NNS|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ are|be|VBP|_ available|available|JJ|_ in|in|IN|_ Bioconductor|Bioconductor|NNP|_ -LRB-|-lrb-|-LRB-|_ www.bioconductor.org|www.bioconductor.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ gene|gene|NN|_ expresion|expresion|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ from|from|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ of|of|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.6|0.6|CD|_ -LRB-|-lrb-|-LRB-|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 10|10|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ and|and|CC|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ STOP|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.7|4.7|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 20|20|CD|_ min|min|NN|_ incubation|incubation|NN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ and|and|CC|_ 7000|7000|CD|_ x|x|CC|_ g|g|NN|_ in|in|IN|_ a|a|DT|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ from|from|IN|_ one|one|CD|_ aliquot|aliquot|NN|_ were|be|VBD|_ gently|gently|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAProtect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ further|further|JJ|_ stabilize|stabilize|VB|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ Remaining|remain|VBG|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ placed|place|VBN|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ for|for|IN|_ archival|archival|JJ|_ storage|storage|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ on|on|IN|_ column|column|NN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ '|'|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ 23S|23s|NN|_ and|and|CC|_ 16S|16s|NN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ subtractive|subtractive|JJ|_ hybridization|hybridization|NN|_ using|use|VBG|_ the|the|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ modifications|modification|NNS|_ .|.|.|_ Compared|compare|VBN|_ with|with|IN|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ ,|,|,|_ 50|50|CD|_ %|%|NN|_ more|more|JJR|_ capture|capture|NN|_ oligonucleotides|oligonucleotide|NNS|_ and|and|CC|_ magnetic|magnetic|JJ|_ beads|bead|NNS|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ 5S|5s|NN|_ rRNAs|rrna|NNS|_ -LRB-|-lrb-|-LRB-|_ 120|120|CD|_ nt|nt|NNS|_ in|in|IN|_ length|length|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ during|during|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ on|on|IN|_ column|column|NN|_ .|.|.|_ Specifically|specifically|RB|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ depletion|depletion|NN|_ on|on|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ -LRB-|-lrb-|-LRB-|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ triplicate|triplicate|NN|_ to|to|TO|_ an|a|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ .|.|.|_ RT-PCR|rt-pcr|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ SuperScript|SuperScript|NNP|_ ®|®|NNP|_ II|II|NNP|_ One-step|one-step|JJ|_ RT-PCR|rt-pcr|NN|_ reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq2000|hiseq2000|NN|_ platform|platform|NN|_ with|with|IN|_ a|a|DT|_ paired-end|paired-end|NN|_ protocol|protocol|NN|_ and|and|CC|_ read|read|VB|_ lengths|length|NNS|_ of|of|IN|_ 50|50|CD|_ nt|nt|NNS|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ measured|measure|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Fluorometer|Fluorometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ removal|removal|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ and|and|CC|_ cDNA|cdna|NN|_ library|library|NN|_ validation|validation|NN|_ were|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strains|strain|NNS|_ E.coli|e.coli|JJ|_ C|c|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 4860|4860|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ Crooks|crook|NNS|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 1576|1576|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DH5α|dh5α|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 6897|6897|CD|_ -RRB-|-rrb-|-RRB-|_ E.|e.|FW|_ coli|coli|FW|_ W|w|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 1116|1116|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 5911|5911|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ DSMZ-German|DSMZ-German|NNP|_ Collection|Collection|NNP|_ of|of|IN|_ Microorganism|Microorganism|NNP|_ and|and|CC|_ Cell|cell|NN|_ Cultures|culture|NNS|_ ;|;|:|_ E.|e.|FW|_ coli|coli|FW|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ purchased|purchase|VBN|_ as|as|IN|_ competent|competent|JJ|_ cells|cell|NNS|_ from|from|IN|_ Agilent|Agilent|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ ATCC|atcc|NN|_ 700926|700926|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ Na2HPO4|na2hpo4|NN|_ x|x|NN|_ 7H2O|7h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 6.8|6.8|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ KH2PO4|kh2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NH4Cl|nh4cl|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ mmol|mmol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mmol|mmol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ trace|trace|NN|_ elements|element|NNS|_ ,|,|,|_ Wolf|Wolf|NNP|_ 's|'s|POS|_ vitamin|vitamin|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_ L-1|l-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Anoxic|anoxic|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP was|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ flushing|flush|VBG|_ solution|solution|NN|_ with|with|IN|_ oxygen|oxygen|NN|_ free|free|JJ|_ nitrogen|nitrogen|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ of|of|IN|_ each|each|DT|_ of|of|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ optical|optical|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ or|or|CC|_ 300|300|CD|_ ml|ml|NN|_ oxygen-free|oxygen-free|JJ|_ sealed|sealed|JJ|_ bottles|bottle|NNS|_ containing|contain|VBG|_ 50|50|CD|_ ml|ml|NN|_ glucose-M9|glucose-m9|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Crooks|crook|NNS|_ _|_|VBP|_ anaero|anaero|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crooks|crook|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strains|strain|NNS|_ E.coli|e.coli|JJ|_ C|c|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 4860|4860|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ Crooks|crook|NNS|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 1576|1576|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DH5α|dh5α|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 6897|6897|CD|_ -RRB-|-rrb-|-RRB-|_ E.|e.|FW|_ coli|coli|FW|_ W|w|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 1116|1116|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 5911|5911|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ DSMZ-German|DSMZ-German|NNP|_ Collection|Collection|NNP|_ of|of|IN|_ Microorganism|Microorganism|NNP|_ and|and|CC|_ Cell|cell|NN|_ Cultures|culture|NNS|_ ;|;|:|_ E.|e.|FW|_ coli|coli|FW|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ purchased|purchase|VBN|_ as|as|IN|_ competent|competent|JJ|_ cells|cell|NNS|_ from|from|IN|_ Agilent|Agilent|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ ATCC|atcc|NN|_ 700926|700926|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ Na2HPO4|na2hpo4|NN|_ x|x|NN|_ 7H2O|7h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 6.8|6.8|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ KH2PO4|kh2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NH4Cl|nh4cl|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ mmol|mmol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mmol|mmol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ trace|trace|NN|_ elements|element|NNS|_ ,|,|,|_ Wolf|Wolf|NNP|_ 's|'s|POS|_ vitamin|vitamin|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_ L-1|l-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Anoxic|anoxic|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP was|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ flushing|flush|VBG|_ solution|solution|NN|_ with|with|IN|_ oxygen|oxygen|NN|_ free|free|JJ|_ nitrogen|nitrogen|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ of|of|IN|_ each|each|DT|_ of|of|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ optical|optical|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ or|or|CC|_ 300|300|CD|_ ml|ml|NN|_ oxygen-free|oxygen-free|JJ|_ sealed|sealed|JJ|_ bottles|bottle|NNS|_ containing|contain|VBG|_ 50|50|CD|_ ml|ml|NN|_ glucose-M9|glucose-m9|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Crooks|crook|NNS|_ _|_|VBP|_ anaero|anaero|NN|_
Jonathan|Jonathan|NNP|_ ,|,|,|_ ,|,|,|_ Monk|Monk|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Torrent|Torrent|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5|5|CD|_ software|software|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Alignment|alignment|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ TMAP|tmap|NN|_ map4|map4|NN|_ algorithm|algorithm|NN|_ with|with|IN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ soft-clipping|soft-clipping|JJ|_ and|and|CC|_ a|a|DT|_ minimum|minimum|JJ|_ seed|seed|NN|_ length|length|NN|_ of|of|IN|_ 20|20|CD|_ nt|nt|NNS|_
The|the|DT|_ total|total|JJ|_ sequencing|sequencing|NN|_ base|base|NN|_ pair|pair|NN|_ coverage|coverage|NN|_ for|for|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ was|be|VBD|_ summed|sum|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ total|total|JJ|_ coverage|coverage|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ and|and|CC|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Wu|Wu|NNP|_ et|et|FW|_ al.|al.|FW|_ 2015|2015|CD|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ Nov|Nov|NNP|_ 6|6|CD|_ ;|;|:|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ 11|11|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e1005655|e1005655|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ NCBI|NCBI|NNP|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ File|file|VB|_ with|with|IN|_ normalized|normalize|VBN|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ comparison|comparison|NN|_ of|of|IN|_ expression|expression|NN|_ in|in|IN|_ antibiotic|antibiotic|JJ|_ treated|treat|VBN|_ to|to|TO|_ untreated|untreated|JJ|_ cells|cell|NNS|_ .|.|.|_
Briefly|briefly|RB|_ ,|,|,|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ mixing|mix|VBG|_ the|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ in|in|IN|_ 1/2|1/2|CD|_ volume|volume|NN|_ of|of|IN|_ 99|99|CD|_ °C|°c|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 16|16|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ made|make|VBN|_ in|in|IN|_ RNAse-free|rnase-free|JJ|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 1|1|CD|_ volume|volume|NN|_ of|of|IN|_ 65|65|CD|_ °C|°c|NN|_ acid|acid|NN|_ phenol/chloroform|phenol/chloroform|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ once|once|RB|_ in|in|IN|_ chloroform/isoamyl|chloroform/isoamyl|JJ|_ alcohol|alcohol|NN|_ ,|,|,|_ and|and|CC|_ precipitated|precipitate|VBD|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ dried|dry|VBD|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_ Final|final|JJ|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ with|with|IN|_ 100|100|CD|_ µL|µl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ kit|kit|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ manual|manual|NN|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ twice|twice|JJ|_ amount|amount|NN|_ of|of|IN|_ recommended|recommend|VBN|_ DNase|dnase|NN|_ inactivation|inactivation|NN|_ reagent|reagent|NN|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ DNA-free|dna-free|JJ|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ either|either|CC|_ native|native|JJ|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ on|on|IN|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ chip|chip|NN|_ .|.|.|_
Ion|Ion|NNP|_ Xpress|Xpress|NNP|_ barcoded|barcode|VBD|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ Magnatic|Magnatic|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IonXpress|ionxpress|NN|_ RNA-seq|rna-seq|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ directions|direction|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ untreated|untreated|JJ|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
Mee-Ngan|mee-ngan|NN|_ ,|,|,|_ F.|F.|NNP|_ ,|,|,|_ Yap|Yap|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Torrent|Torrent|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5|5|CD|_ software|software|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Alignment|alignment|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ TMAP|tmap|NN|_ map4|map4|NN|_ algorithm|algorithm|NN|_ with|with|IN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ soft-clipping|soft-clipping|JJ|_ and|and|CC|_ a|a|DT|_ minimum|minimum|JJ|_ seed|seed|NN|_ length|length|NN|_ of|of|IN|_ 20|20|CD|_ nt|nt|NNS|_
The|the|DT|_ total|total|JJ|_ sequencing|sequencing|NN|_ base|base|NN|_ pair|pair|NN|_ coverage|coverage|NN|_ for|for|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ was|be|VBD|_ summed|sum|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ total|total|JJ|_ coverage|coverage|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ and|and|CC|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Wu|Wu|NNP|_ et|et|FW|_ al.|al.|FW|_ 2015|2015|CD|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ Nov|Nov|NNP|_ 6|6|CD|_ ;|;|:|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ 11|11|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e1005655|e1005655|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ NCBI|NCBI|NNP|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ File|file|VB|_ with|with|IN|_ normalized|normalize|VBN|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ comparison|comparison|NN|_ of|of|IN|_ expression|expression|NN|_ in|in|IN|_ antibiotic|antibiotic|JJ|_ treated|treat|VBN|_ to|to|TO|_ untreated|untreated|JJ|_ cells|cell|NNS|_ .|.|.|_
Briefly|briefly|RB|_ ,|,|,|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ mixing|mix|VBG|_ the|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ in|in|IN|_ 1/2|1/2|CD|_ volume|volume|NN|_ of|of|IN|_ 99|99|CD|_ °C|°c|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 16|16|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ made|make|VBN|_ in|in|IN|_ RNAse-free|rnase-free|JJ|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 1|1|CD|_ volume|volume|NN|_ of|of|IN|_ 65|65|CD|_ °C|°c|NN|_ acid|acid|NN|_ phenol/chloroform|phenol/chloroform|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ once|once|RB|_ in|in|IN|_ chloroform/isoamyl|chloroform/isoamyl|JJ|_ alcohol|alcohol|NN|_ ,|,|,|_ and|and|CC|_ precipitated|precipitate|VBD|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ dried|dry|VBD|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_ Final|final|JJ|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ with|with|IN|_ 100|100|CD|_ µL|µl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ kit|kit|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ manual|manual|NN|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ twice|twice|JJ|_ amount|amount|NN|_ of|of|IN|_ recommended|recommend|VBN|_ DNase|dnase|NN|_ inactivation|inactivation|NN|_ reagent|reagent|NN|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ DNA-free|dna-free|JJ|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ either|either|CC|_ native|native|JJ|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ on|on|IN|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ chip|chip|NN|_ .|.|.|_
Ion|Ion|NNP|_ Xpress|Xpress|NNP|_ barcoded|barcode|VBD|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ Magnatic|Magnatic|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IonXpress|ionxpress|NN|_ RNA-seq|rna-seq|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ directions|direction|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ untreated|untreated|JJ|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
Mee-Ngan|mee-ngan|NN|_ ,|,|,|_ F.|F.|NNP|_ ,|,|,|_ Yap|Yap|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Torrent|Torrent|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5|5|CD|_ software|software|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Alignment|alignment|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ TMAP|tmap|NN|_ map4|map4|NN|_ algorithm|algorithm|NN|_ with|with|IN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ soft-clipping|soft-clipping|JJ|_ and|and|CC|_ a|a|DT|_ minimum|minimum|JJ|_ seed|seed|NN|_ length|length|NN|_ of|of|IN|_ 20|20|CD|_ nt|nt|NNS|_
The|the|DT|_ total|total|JJ|_ sequencing|sequencing|NN|_ base|base|NN|_ pair|pair|NN|_ coverage|coverage|NN|_ for|for|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ was|be|VBD|_ summed|sum|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ total|total|JJ|_ coverage|coverage|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ and|and|CC|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Wu|Wu|NNP|_ et|et|FW|_ al.|al.|FW|_ 2015|2015|CD|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ Nov|Nov|NNP|_ 6|6|CD|_ ;|;|:|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ 11|11|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e1005655|e1005655|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ NCBI|NCBI|NNP|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ File|file|VB|_ with|with|IN|_ normalized|normalize|VBN|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ comparison|comparison|NN|_ of|of|IN|_ expression|expression|NN|_ in|in|IN|_ antibiotic|antibiotic|JJ|_ treated|treat|VBN|_ to|to|TO|_ untreated|untreated|JJ|_ cells|cell|NNS|_ .|.|.|_
Briefly|briefly|RB|_ ,|,|,|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ mixing|mix|VBG|_ the|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ in|in|IN|_ 1/2|1/2|CD|_ volume|volume|NN|_ of|of|IN|_ 99|99|CD|_ °C|°c|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 16|16|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ made|make|VBN|_ in|in|IN|_ RNAse-free|rnase-free|JJ|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 1|1|CD|_ volume|volume|NN|_ of|of|IN|_ 65|65|CD|_ °C|°c|NN|_ acid|acid|NN|_ phenol/chloroform|phenol/chloroform|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ once|once|RB|_ in|in|IN|_ chloroform/isoamyl|chloroform/isoamyl|JJ|_ alcohol|alcohol|NN|_ ,|,|,|_ and|and|CC|_ precipitated|precipitate|VBD|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ dried|dry|VBD|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_ Final|final|JJ|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ with|with|IN|_ 100|100|CD|_ µL|µl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ kit|kit|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ manual|manual|NN|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ twice|twice|JJ|_ amount|amount|NN|_ of|of|IN|_ recommended|recommend|VBN|_ DNase|dnase|NN|_ inactivation|inactivation|NN|_ reagent|reagent|NN|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ DNA-free|dna-free|JJ|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ either|either|CC|_ native|native|JJ|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ on|on|IN|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ chip|chip|NN|_ .|.|.|_
Ion|Ion|NNP|_ Xpress|Xpress|NNP|_ barcoded|barcode|VBD|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ Magnatic|Magnatic|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IonXpress|ionxpress|NN|_ RNA-seq|rna-seq|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ directions|direction|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ untreated|untreated|JJ|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
Mee-Ngan|mee-ngan|NN|_ ,|,|,|_ F.|F.|NNP|_ ,|,|,|_ Yap|Yap|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Torrent|Torrent|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5|5|CD|_ software|software|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Alignment|alignment|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ TMAP|tmap|NN|_ map4|map4|NN|_ algorithm|algorithm|NN|_ with|with|IN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ soft-clipping|soft-clipping|JJ|_ and|and|CC|_ a|a|DT|_ minimum|minimum|JJ|_ seed|seed|NN|_ length|length|NN|_ of|of|IN|_ 20|20|CD|_ nt|nt|NNS|_
The|the|DT|_ total|total|JJ|_ sequencing|sequencing|NN|_ base|base|NN|_ pair|pair|NN|_ coverage|coverage|NN|_ for|for|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ was|be|VBD|_ summed|sum|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ total|total|JJ|_ coverage|coverage|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ and|and|CC|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Wu|Wu|NNP|_ et|et|FW|_ al.|al.|FW|_ 2015|2015|CD|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ Nov|Nov|NNP|_ 6|6|CD|_ ;|;|:|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ 11|11|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e1005655|e1005655|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ NCBI|NCBI|NNP|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ File|file|VB|_ with|with|IN|_ normalized|normalize|VBN|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ comparison|comparison|NN|_ of|of|IN|_ expression|expression|NN|_ in|in|IN|_ antibiotic|antibiotic|JJ|_ treated|treat|VBN|_ to|to|TO|_ untreated|untreated|JJ|_ cells|cell|NNS|_ .|.|.|_
Briefly|briefly|RB|_ ,|,|,|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ mixing|mix|VBG|_ the|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ in|in|IN|_ 1/2|1/2|CD|_ volume|volume|NN|_ of|of|IN|_ 99|99|CD|_ °C|°c|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 16|16|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ made|make|VBN|_ in|in|IN|_ RNAse-free|rnase-free|JJ|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 1|1|CD|_ volume|volume|NN|_ of|of|IN|_ 65|65|CD|_ °C|°c|NN|_ acid|acid|NN|_ phenol/chloroform|phenol/chloroform|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ once|once|RB|_ in|in|IN|_ chloroform/isoamyl|chloroform/isoamyl|JJ|_ alcohol|alcohol|NN|_ ,|,|,|_ and|and|CC|_ precipitated|precipitate|VBD|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ dried|dry|VBD|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_ Final|final|JJ|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ with|with|IN|_ 100|100|CD|_ µL|µl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ kit|kit|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ manual|manual|NN|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ twice|twice|JJ|_ amount|amount|NN|_ of|of|IN|_ recommended|recommend|VBN|_ DNase|dnase|NN|_ inactivation|inactivation|NN|_ reagent|reagent|NN|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ DNA-free|dna-free|JJ|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ either|either|CC|_ native|native|JJ|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ on|on|IN|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ chip|chip|NN|_ .|.|.|_
Ion|Ion|NNP|_ Xpress|Xpress|NNP|_ barcoded|barcode|VBD|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ Magnatic|Magnatic|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IonXpress|ionxpress|NN|_ RNA-seq|rna-seq|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ directions|direction|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ erythromycin|erythromycin|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
Mee-Ngan|mee-ngan|NN|_ ,|,|,|_ F.|F.|NNP|_ ,|,|,|_ Yap|Yap|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Torrent|Torrent|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5|5|CD|_ software|software|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Alignment|alignment|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ TMAP|tmap|NN|_ map4|map4|NN|_ algorithm|algorithm|NN|_ with|with|IN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ soft-clipping|soft-clipping|JJ|_ and|and|CC|_ a|a|DT|_ minimum|minimum|JJ|_ seed|seed|NN|_ length|length|NN|_ of|of|IN|_ 20|20|CD|_ nt|nt|NNS|_
The|the|DT|_ total|total|JJ|_ sequencing|sequencing|NN|_ base|base|NN|_ pair|pair|NN|_ coverage|coverage|NN|_ for|for|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ was|be|VBD|_ summed|sum|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ total|total|JJ|_ coverage|coverage|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ and|and|CC|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Wu|Wu|NNP|_ et|et|FW|_ al.|al.|FW|_ 2015|2015|CD|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ Nov|Nov|NNP|_ 6|6|CD|_ ;|;|:|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ 11|11|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e1005655|e1005655|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ NCBI|NCBI|NNP|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ File|file|VB|_ with|with|IN|_ normalized|normalize|VBN|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ comparison|comparison|NN|_ of|of|IN|_ expression|expression|NN|_ in|in|IN|_ antibiotic|antibiotic|JJ|_ treated|treat|VBN|_ to|to|TO|_ untreated|untreated|JJ|_ cells|cell|NNS|_ .|.|.|_
Briefly|briefly|RB|_ ,|,|,|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ mixing|mix|VBG|_ the|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ in|in|IN|_ 1/2|1/2|CD|_ volume|volume|NN|_ of|of|IN|_ 99|99|CD|_ °C|°c|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 16|16|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ made|make|VBN|_ in|in|IN|_ RNAse-free|rnase-free|JJ|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 1|1|CD|_ volume|volume|NN|_ of|of|IN|_ 65|65|CD|_ °C|°c|NN|_ acid|acid|NN|_ phenol/chloroform|phenol/chloroform|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ once|once|RB|_ in|in|IN|_ chloroform/isoamyl|chloroform/isoamyl|JJ|_ alcohol|alcohol|NN|_ ,|,|,|_ and|and|CC|_ precipitated|precipitate|VBD|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ dried|dry|VBD|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_ Final|final|JJ|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ with|with|IN|_ 100|100|CD|_ µL|µl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ kit|kit|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ manual|manual|NN|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ twice|twice|JJ|_ amount|amount|NN|_ of|of|IN|_ recommended|recommend|VBN|_ DNase|dnase|NN|_ inactivation|inactivation|NN|_ reagent|reagent|NN|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ DNA-free|dna-free|JJ|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ either|either|CC|_ native|native|JJ|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ on|on|IN|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ chip|chip|NN|_ .|.|.|_
Ion|Ion|NNP|_ Xpress|Xpress|NNP|_ barcoded|barcode|VBD|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ Magnatic|Magnatic|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IonXpress|ionxpress|NN|_ RNA-seq|rna-seq|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ directions|direction|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ erythromycin|erythromycin|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
Mee-Ngan|mee-ngan|NN|_ ,|,|,|_ F.|F.|NNP|_ ,|,|,|_ Yap|Yap|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Torrent|Torrent|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5|5|CD|_ software|software|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Alignment|alignment|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ TMAP|tmap|NN|_ map4|map4|NN|_ algorithm|algorithm|NN|_ with|with|IN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ soft-clipping|soft-clipping|JJ|_ and|and|CC|_ a|a|DT|_ minimum|minimum|JJ|_ seed|seed|NN|_ length|length|NN|_ of|of|IN|_ 20|20|CD|_ nt|nt|NNS|_
The|the|DT|_ total|total|JJ|_ sequencing|sequencing|NN|_ base|base|NN|_ pair|pair|NN|_ coverage|coverage|NN|_ for|for|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ was|be|VBD|_ summed|sum|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ total|total|JJ|_ coverage|coverage|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ and|and|CC|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Wu|Wu|NNP|_ et|et|FW|_ al.|al.|FW|_ 2015|2015|CD|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ Nov|Nov|NNP|_ 6|6|CD|_ ;|;|:|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ 11|11|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e1005655|e1005655|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ NCBI|NCBI|NNP|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ File|file|VB|_ with|with|IN|_ normalized|normalize|VBN|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ comparison|comparison|NN|_ of|of|IN|_ expression|expression|NN|_ in|in|IN|_ antibiotic|antibiotic|JJ|_ treated|treat|VBN|_ to|to|TO|_ untreated|untreated|JJ|_ cells|cell|NNS|_ .|.|.|_
Briefly|briefly|RB|_ ,|,|,|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ mixing|mix|VBG|_ the|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ in|in|IN|_ 1/2|1/2|CD|_ volume|volume|NN|_ of|of|IN|_ 99|99|CD|_ °C|°c|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 16|16|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ made|make|VBN|_ in|in|IN|_ RNAse-free|rnase-free|JJ|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 1|1|CD|_ volume|volume|NN|_ of|of|IN|_ 65|65|CD|_ °C|°c|NN|_ acid|acid|NN|_ phenol/chloroform|phenol/chloroform|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ once|once|RB|_ in|in|IN|_ chloroform/isoamyl|chloroform/isoamyl|JJ|_ alcohol|alcohol|NN|_ ,|,|,|_ and|and|CC|_ precipitated|precipitate|VBD|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ dried|dry|VBD|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_ Final|final|JJ|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ with|with|IN|_ 100|100|CD|_ µL|µl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ kit|kit|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ manual|manual|NN|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ twice|twice|JJ|_ amount|amount|NN|_ of|of|IN|_ recommended|recommend|VBN|_ DNase|dnase|NN|_ inactivation|inactivation|NN|_ reagent|reagent|NN|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ DNA-free|dna-free|JJ|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ either|either|CC|_ native|native|JJ|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ on|on|IN|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ chip|chip|NN|_ .|.|.|_
Ion|Ion|NNP|_ Xpress|Xpress|NNP|_ barcoded|barcode|VBD|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ Magnatic|Magnatic|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IonXpress|ionxpress|NN|_ RNA-seq|rna-seq|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ directions|direction|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ erythromycin|erythromycin|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
Mee-Ngan|mee-ngan|NN|_ ,|,|,|_ F.|F.|NNP|_ ,|,|,|_ Yap|Yap|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Torrent|Torrent|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5|5|CD|_ software|software|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Alignment|alignment|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ TMAP|tmap|NN|_ map4|map4|NN|_ algorithm|algorithm|NN|_ with|with|IN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ soft-clipping|soft-clipping|JJ|_ and|and|CC|_ a|a|DT|_ minimum|minimum|JJ|_ seed|seed|NN|_ length|length|NN|_ of|of|IN|_ 20|20|CD|_ nt|nt|NNS|_
The|the|DT|_ total|total|JJ|_ sequencing|sequencing|NN|_ base|base|NN|_ pair|pair|NN|_ coverage|coverage|NN|_ for|for|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ was|be|VBD|_ summed|sum|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ total|total|JJ|_ coverage|coverage|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ and|and|CC|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Wu|Wu|NNP|_ et|et|FW|_ al.|al.|FW|_ 2015|2015|CD|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ Nov|Nov|NNP|_ 6|6|CD|_ ;|;|:|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ 11|11|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e1005655|e1005655|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ NCBI|NCBI|NNP|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ File|file|VB|_ with|with|IN|_ normalized|normalize|VBN|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ comparison|comparison|NN|_ of|of|IN|_ expression|expression|NN|_ in|in|IN|_ antibiotic|antibiotic|JJ|_ treated|treat|VBN|_ to|to|TO|_ untreated|untreated|JJ|_ cells|cell|NNS|_ .|.|.|_
Briefly|briefly|RB|_ ,|,|,|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ mixing|mix|VBG|_ the|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ in|in|IN|_ 1/2|1/2|CD|_ volume|volume|NN|_ of|of|IN|_ 99|99|CD|_ °C|°c|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 16|16|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ made|make|VBN|_ in|in|IN|_ RNAse-free|rnase-free|JJ|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 1|1|CD|_ volume|volume|NN|_ of|of|IN|_ 65|65|CD|_ °C|°c|NN|_ acid|acid|NN|_ phenol/chloroform|phenol/chloroform|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ once|once|RB|_ in|in|IN|_ chloroform/isoamyl|chloroform/isoamyl|JJ|_ alcohol|alcohol|NN|_ ,|,|,|_ and|and|CC|_ precipitated|precipitate|VBD|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ dried|dry|VBD|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_ Final|final|JJ|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ with|with|IN|_ 100|100|CD|_ µL|µl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ kit|kit|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ manual|manual|NN|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ twice|twice|JJ|_ amount|amount|NN|_ of|of|IN|_ recommended|recommend|VBN|_ DNase|dnase|NN|_ inactivation|inactivation|NN|_ reagent|reagent|NN|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ DNA-free|dna-free|JJ|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ either|either|CC|_ native|native|JJ|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ on|on|IN|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ chip|chip|NN|_ .|.|.|_
Ion|Ion|NNP|_ Xpress|Xpress|NNP|_ barcoded|barcode|VBD|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ Magnatic|Magnatic|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IonXpress|ionxpress|NN|_ RNA-seq|rna-seq|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ directions|direction|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ clindamycin|clindamycin|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
Mee-Ngan|mee-ngan|NN|_ ,|,|,|_ F.|F.|NNP|_ ,|,|,|_ Yap|Yap|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Torrent|Torrent|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5|5|CD|_ software|software|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Alignment|alignment|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ TMAP|tmap|NN|_ map4|map4|NN|_ algorithm|algorithm|NN|_ with|with|IN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ soft-clipping|soft-clipping|JJ|_ and|and|CC|_ a|a|DT|_ minimum|minimum|JJ|_ seed|seed|NN|_ length|length|NN|_ of|of|IN|_ 20|20|CD|_ nt|nt|NNS|_
The|the|DT|_ total|total|JJ|_ sequencing|sequencing|NN|_ base|base|NN|_ pair|pair|NN|_ coverage|coverage|NN|_ for|for|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ was|be|VBD|_ summed|sum|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ total|total|JJ|_ coverage|coverage|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ and|and|CC|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Wu|Wu|NNP|_ et|et|FW|_ al.|al.|FW|_ 2015|2015|CD|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ Nov|Nov|NNP|_ 6|6|CD|_ ;|;|:|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ 11|11|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e1005655|e1005655|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ NCBI|NCBI|NNP|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ File|file|VB|_ with|with|IN|_ normalized|normalize|VBN|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ comparison|comparison|NN|_ of|of|IN|_ expression|expression|NN|_ in|in|IN|_ antibiotic|antibiotic|JJ|_ treated|treat|VBN|_ to|to|TO|_ untreated|untreated|JJ|_ cells|cell|NNS|_ .|.|.|_
Briefly|briefly|RB|_ ,|,|,|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ mixing|mix|VBG|_ the|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ in|in|IN|_ 1/2|1/2|CD|_ volume|volume|NN|_ of|of|IN|_ 99|99|CD|_ °C|°c|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 16|16|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ made|make|VBN|_ in|in|IN|_ RNAse-free|rnase-free|JJ|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 1|1|CD|_ volume|volume|NN|_ of|of|IN|_ 65|65|CD|_ °C|°c|NN|_ acid|acid|NN|_ phenol/chloroform|phenol/chloroform|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ once|once|RB|_ in|in|IN|_ chloroform/isoamyl|chloroform/isoamyl|JJ|_ alcohol|alcohol|NN|_ ,|,|,|_ and|and|CC|_ precipitated|precipitate|VBD|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ dried|dry|VBD|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_ Final|final|JJ|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ with|with|IN|_ 100|100|CD|_ µL|µl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ kit|kit|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ manual|manual|NN|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ twice|twice|JJ|_ amount|amount|NN|_ of|of|IN|_ recommended|recommend|VBN|_ DNase|dnase|NN|_ inactivation|inactivation|NN|_ reagent|reagent|NN|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ DNA-free|dna-free|JJ|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ either|either|CC|_ native|native|JJ|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ on|on|IN|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ chip|chip|NN|_ .|.|.|_
Ion|Ion|NNP|_ Xpress|Xpress|NNP|_ barcoded|barcode|VBD|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ Magnatic|Magnatic|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IonXpress|ionxpress|NN|_ RNA-seq|rna-seq|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ directions|direction|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ clindamycin|clindamycin|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
Mee-Ngan|mee-ngan|NN|_ ,|,|,|_ F.|F.|NNP|_ ,|,|,|_ Yap|Yap|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Torrent|Torrent|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5|5|CD|_ software|software|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Alignment|alignment|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ TMAP|tmap|NN|_ map4|map4|NN|_ algorithm|algorithm|NN|_ with|with|IN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ soft-clipping|soft-clipping|JJ|_ and|and|CC|_ a|a|DT|_ minimum|minimum|JJ|_ seed|seed|NN|_ length|length|NN|_ of|of|IN|_ 20|20|CD|_ nt|nt|NNS|_
The|the|DT|_ total|total|JJ|_ sequencing|sequencing|NN|_ base|base|NN|_ pair|pair|NN|_ coverage|coverage|NN|_ for|for|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ was|be|VBD|_ summed|sum|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ total|total|JJ|_ coverage|coverage|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ and|and|CC|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Wu|Wu|NNP|_ et|et|FW|_ al.|al.|FW|_ 2015|2015|CD|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ Nov|Nov|NNP|_ 6|6|CD|_ ;|;|:|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ 11|11|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e1005655|e1005655|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ NCBI|NCBI|NNP|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ File|file|VB|_ with|with|IN|_ normalized|normalize|VBN|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ comparison|comparison|NN|_ of|of|IN|_ expression|expression|NN|_ in|in|IN|_ antibiotic|antibiotic|JJ|_ treated|treat|VBN|_ to|to|TO|_ untreated|untreated|JJ|_ cells|cell|NNS|_ .|.|.|_
Briefly|briefly|RB|_ ,|,|,|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ mixing|mix|VBG|_ the|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ in|in|IN|_ 1/2|1/2|CD|_ volume|volume|NN|_ of|of|IN|_ 99|99|CD|_ °C|°c|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 16|16|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ made|make|VBN|_ in|in|IN|_ RNAse-free|rnase-free|JJ|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 1|1|CD|_ volume|volume|NN|_ of|of|IN|_ 65|65|CD|_ °C|°c|NN|_ acid|acid|NN|_ phenol/chloroform|phenol/chloroform|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ once|once|RB|_ in|in|IN|_ chloroform/isoamyl|chloroform/isoamyl|JJ|_ alcohol|alcohol|NN|_ ,|,|,|_ and|and|CC|_ precipitated|precipitate|VBD|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ 70|70|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ dried|dry|VBD|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_ Final|final|JJ|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ with|with|IN|_ 100|100|CD|_ µL|µl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ kit|kit|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ manual|manual|NN|_ ,|,|,|_ except|except|IN|_ that|that|DT|_ twice|twice|JJ|_ amount|amount|NN|_ of|of|IN|_ recommended|recommend|VBN|_ DNase|dnase|NN|_ inactivation|inactivation|NN|_ reagent|reagent|NN|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ DNA-free|dna-free|JJ|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ either|either|CC|_ native|native|JJ|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ on|on|IN|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ chip|chip|NN|_ .|.|.|_
Ion|Ion|NNP|_ Xpress|Xpress|NNP|_ barcoded|barcode|VBD|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ Magnatic|Magnatic|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IonXpress|ionxpress|NN|_ RNA-seq|rna-seq|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ directions|direction|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ clindamycin|clindamycin|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg/mL|100µg/ml|NN|_ Erythromycin|erythromycin|NN|_ or|or|CC|_ 50|50|CD|_ µg/mL|µg/ml|NN|_ Clindamycin|clindamycin|NN|_ in|in|IN|_ 70|70|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 1|1|CD|_ mL|ml|NN|_ samples|sample|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ .|.|.|_ Ref|Ref|NNP|_ :|:|:|_ Chuang|Chuang|NNP|_ SE|se|NN|_ ,|,|,|_ Daniels|Daniels|NNP|_ DL|DL|NNP|_ ,|,|,|_ and|and|CC|_ Blattner|Blattner|NNP|_ FR|fr|NN|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ Global|global|JJ|_ regulation|regulation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism .|.|.|_ J.|J.|NNP|_ Bacteriol|Bacteriol|NNP|_ .|.|.|_ 175:2026-2036|175:2026-2036|CD|_ .|.|.|_
Mee-Ngan|mee-ngan|NN|_ ,|,|,|_ F.|F.|NNP|_ ,|,|,|_ Yap|Yap|NNP|_
Sequence|sequence|NN|_ data|datum|NNS|_ from|from|IN|_ BGI|BGI|NNP|_ had|have|VBD|_ been|be|VBN|_ filtered|filter|VBN|_ to|to|TO|_ remove|remove|VB|_ reads|read|VBZ|_ containing|contain|VBG|_ ≥|≥|SYM|_ 10|10|CD|_ %|%|NN|_ unreadable|unreadable|JJ|_ bases|basis|NNS|_ ,|,|,|_ ≥|≥|SYM|_ 20|20|CD|_ %|%|NN|_ low|low|JJ|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ ≤|≤|CD|_ Q20|q20|NN|_ -RRB-|-rrb-|-RRB-|_ bases|basis|NNS|_ ,|,|,|_ adapter|adapter|NN|_ contamination|contamination|NN|_ or|or|CC|_ duplicate|duplicate|VB|_ read-pairs|read-pairs|JJ|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ reads|read|VBZ|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Andrews|Andrews|NNP|_ S|s|NN|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ any|any|DT|_ reads|read|VBZ|_ with|with|IN|_ a|a|DT|_ quality|quality|NN|_ score|score|NN|_ ≤|≤|CD|_ Q28|q28|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trim|Trim|NNP|_ Galore|Galore|NNP|_ !|!|.|_ -LRB-|-lrb-|-LRB-|_ Krueger|krueger|NN|_ F|f|NN|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ B|b|NN|_ &|&|CC|_ Salzberg|Salzberg|NNP|_ SL|SL|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ ,|,|,|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ sequence|sequence|NN|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ ,|,|,|_ transfer|transfer|NN|_ RNA|rna|NN|_ and|and|CC|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ sequences|sequence|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ EDGE-Pro|edge-pro|NN|_ -LRB-|-lrb-|-LRB-|_ Magoc|magoc|NN|_ T|t|NN|_ ,|,|,|_ Wood|Wood|NNP|_ D|D|NNP|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ SL|SL|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ environments|environment|NNS|_ was|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ Love|love|NN|_ M|m|NN|_ ,|,|,|_ Huber|Huber|NNP|_ W|W|NNP|_ and|and|CC|_ Anders|Anders|NNP|_ S|s|NN|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ str|str|NN|_ .|.|.|_ REL606|rel606|NN|_ ;|;|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ harvested|harvest|VBN|_ cultures|culture|NNS|_ using|use|VBG|_ a|a|DT|_ hot|hot|JJ|_ lysis|lysis|NN|_ buffer|buffer|NN|_ and|and|CC|_ acid|acid|NN|_ phenol-based|phenol-based|JJ|_ extraction|extraction|NN|_ method|method|NN|_ and|and|CC|_ isopropanol|isopropanol|NN|_ precipitation|precipitation|NN|_ .|.|.|_ Following|follow|VBG|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ treat|treat|VB|_ the|the|DT|_ samples|sample|NNS|_ as|as|IN|_ per|per|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ split|split|VBN|_ into|into|IN|_ five|five|CD|_ 20|20|CD|_ μL|μl|NN|_ aliquots|aliquot|NNS|_ and|and|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ were|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ each|each|DT|_ aliquot|aliquot|NN|_ .|.|.|_ Following|follow|VBG|_ DNase|dnase|NN|_ treatment|treatment|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ aliquots|aliquot|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ before|before|IN|_ purification|purification|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ measured|measure|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ while|while|IN|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Quant-iT|quant-it|JJ|_ RNA|rna|NN|_ Assay|assay|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ measured|measure|VBN|_ on|on|IN|_ a|a|DT|_ Qubit|Qubit|NNP|_ ®|®|NNP|_ 2.0|2.0|CD|_ fluorometer|fluorometer|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ at|at|IN|_ BGI|BGI|NNP|_ -LRB-|-lrb-|-LRB-|_ Shenzen|Shenzen|NNP|_ ,|,|,|_ China|China|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Aerobic|Aerobic|NNP|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 600|600|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ DM25|dm25|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ of|of|IN|_ 150|150|CD|_ RPM|rpm|NN|_ and|and|CC|_ inoculated|inoculate|VBN|_ with|with|IN|_ 1/100th|1/100th|JJ|_ volume|volume|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 9|9|CD|_ h|h|NN|_ while|while|IN|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 16|16|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Cultured|culture|VBN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ REL4536|rel4536|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stationary|stationary|JJ|_ phase|phase|NN|_
growth|growth|NN|_ environment|environment|NN|_ :|:|:|_ Aerobic|aerobic|JJ|_
Aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 600|600|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ DM25|dm25|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ of|of|IN|_ 150|150|CD|_ RPM|rpm|NN|_ and|and|CC|_ inoculated|inoculate|VBN|_ with|with|IN|_ 1/100th|1/100th|JJ|_ volume|volume|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 9|9|CD|_ h|h|NN|_ while|while|IN|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 16|16|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Cultured|culture|VBN|_ cells|cell|NNS|_
Christina|Christina|NNP|_ ,|,|,|_ ,|,|,|_ Moon|Moon|NNP|_
Sequence|sequence|NN|_ data|datum|NNS|_ from|from|IN|_ BGI|BGI|NNP|_ had|have|VBD|_ been|be|VBN|_ filtered|filter|VBN|_ to|to|TO|_ remove|remove|VB|_ reads|read|VBZ|_ containing|contain|VBG|_ ≥|≥|SYM|_ 10|10|CD|_ %|%|NN|_ unreadable|unreadable|JJ|_ bases|basis|NNS|_ ,|,|,|_ ≥|≥|SYM|_ 20|20|CD|_ %|%|NN|_ low|low|JJ|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ ≤|≤|CD|_ Q20|q20|NN|_ -RRB-|-rrb-|-RRB-|_ bases|basis|NNS|_ ,|,|,|_ adapter|adapter|NN|_ contamination|contamination|NN|_ or|or|CC|_ duplicate|duplicate|VB|_ read-pairs|read-pairs|JJ|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ reads|read|VBZ|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Andrews|Andrews|NNP|_ S|s|NN|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ any|any|DT|_ reads|read|VBZ|_ with|with|IN|_ a|a|DT|_ quality|quality|NN|_ score|score|NN|_ ≤|≤|CD|_ Q28|q28|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trim|Trim|NNP|_ Galore|Galore|NNP|_ !|!|.|_ -LRB-|-lrb-|-LRB-|_ Krueger|krueger|NN|_ F|f|NN|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ B|b|NN|_ &|&|CC|_ Salzberg|Salzberg|NNP|_ SL|SL|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ ,|,|,|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ sequence|sequence|NN|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ ,|,|,|_ transfer|transfer|NN|_ RNA|rna|NN|_ and|and|CC|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ sequences|sequence|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ EDGE-Pro|edge-pro|NN|_ -LRB-|-lrb-|-LRB-|_ Magoc|magoc|NN|_ T|t|NN|_ ,|,|,|_ Wood|Wood|NNP|_ D|D|NNP|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ SL|SL|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ environments|environment|NNS|_ was|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ Love|love|NN|_ M|m|NN|_ ,|,|,|_ Huber|Huber|NNP|_ W|W|NNP|_ and|and|CC|_ Anders|Anders|NNP|_ S|s|NN|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ str|str|NN|_ .|.|.|_ REL606|rel606|NN|_ ;|;|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ harvested|harvest|VBN|_ cultures|culture|NNS|_ using|use|VBG|_ a|a|DT|_ hot|hot|JJ|_ lysis|lysis|NN|_ buffer|buffer|NN|_ and|and|CC|_ acid|acid|NN|_ phenol-based|phenol-based|JJ|_ extraction|extraction|NN|_ method|method|NN|_ and|and|CC|_ isopropanol|isopropanol|NN|_ precipitation|precipitation|NN|_ .|.|.|_ Following|follow|VBG|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ treat|treat|VB|_ the|the|DT|_ samples|sample|NNS|_ as|as|IN|_ per|per|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ split|split|VBN|_ into|into|IN|_ five|five|CD|_ 20|20|CD|_ μL|μl|NN|_ aliquots|aliquot|NNS|_ and|and|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ were|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ each|each|DT|_ aliquot|aliquot|NN|_ .|.|.|_ Following|follow|VBG|_ DNase|dnase|NN|_ treatment|treatment|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ aliquots|aliquot|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ before|before|IN|_ purification|purification|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ measured|measure|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ while|while|IN|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Quant-iT|quant-it|JJ|_ RNA|rna|NN|_ Assay|assay|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ measured|measure|VBN|_ on|on|IN|_ a|a|DT|_ Qubit|Qubit|NNP|_ ®|®|NNP|_ 2.0|2.0|CD|_ fluorometer|fluorometer|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ at|at|IN|_ BGI|BGI|NNP|_ -LRB-|-lrb-|-LRB-|_ Shenzen|Shenzen|NNP|_ ,|,|,|_ China|China|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Aerobic|Aerobic|NNP|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 600|600|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ DM25|dm25|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ of|of|IN|_ 150|150|CD|_ RPM|rpm|NN|_ and|and|CC|_ inoculated|inoculate|VBN|_ with|with|IN|_ 1/100th|1/100th|JJ|_ volume|volume|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 9|9|CD|_ h|h|NN|_ while|while|IN|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 16|16|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Cultured|culture|VBN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ REL4536|rel4536|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stationary|stationary|JJ|_ phase|phase|NN|_
growth|growth|NN|_ environment|environment|NN|_ :|:|:|_ Aerobic|aerobic|JJ|_
Aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 600|600|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ DM25|dm25|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ of|of|IN|_ 150|150|CD|_ RPM|rpm|NN|_ and|and|CC|_ inoculated|inoculate|VBN|_ with|with|IN|_ 1/100th|1/100th|JJ|_ volume|volume|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 9|9|CD|_ h|h|NN|_ while|while|IN|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 16|16|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Cultured|culture|VBN|_ cells|cell|NNS|_
Christina|Christina|NNP|_ ,|,|,|_ ,|,|,|_ Moon|Moon|NNP|_
Sequence|sequence|NN|_ data|datum|NNS|_ from|from|IN|_ BGI|BGI|NNP|_ had|have|VBD|_ been|be|VBN|_ filtered|filter|VBN|_ to|to|TO|_ remove|remove|VB|_ reads|read|VBZ|_ containing|contain|VBG|_ ≥|≥|SYM|_ 10|10|CD|_ %|%|NN|_ unreadable|unreadable|JJ|_ bases|basis|NNS|_ ,|,|,|_ ≥|≥|SYM|_ 20|20|CD|_ %|%|NN|_ low|low|JJ|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ ≤|≤|CD|_ Q20|q20|NN|_ -RRB-|-rrb-|-RRB-|_ bases|basis|NNS|_ ,|,|,|_ adapter|adapter|NN|_ contamination|contamination|NN|_ or|or|CC|_ duplicate|duplicate|VB|_ read-pairs|read-pairs|JJ|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ reads|read|VBZ|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Andrews|Andrews|NNP|_ S|s|NN|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ any|any|DT|_ reads|read|VBZ|_ with|with|IN|_ a|a|DT|_ quality|quality|NN|_ score|score|NN|_ ≤|≤|CD|_ Q28|q28|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trim|Trim|NNP|_ Galore|Galore|NNP|_ !|!|.|_ -LRB-|-lrb-|-LRB-|_ Krueger|krueger|NN|_ F|f|NN|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ B|b|NN|_ &|&|CC|_ Salzberg|Salzberg|NNP|_ SL|SL|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ ,|,|,|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ sequence|sequence|NN|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ ,|,|,|_ transfer|transfer|NN|_ RNA|rna|NN|_ and|and|CC|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ sequences|sequence|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ EDGE-Pro|edge-pro|NN|_ -LRB-|-lrb-|-LRB-|_ Magoc|magoc|NN|_ T|t|NN|_ ,|,|,|_ Wood|Wood|NNP|_ D|D|NNP|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ SL|SL|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
Differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ environments|environment|NNS|_ was|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ Love|love|NN|_ M|m|NN|_ ,|,|,|_ Huber|Huber|NNP|_ W|W|NNP|_ and|and|CC|_ Anders|Anders|NNP|_ S|s|NN|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ str|str|NN|_ .|.|.|_ REL606|rel606|NN|_ ;|;|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ harvested|harvest|VBN|_ cultures|culture|NNS|_ using|use|VBG|_ a|a|DT|_ hot|hot|JJ|_ lysis|lysis|NN|_ buffer|buffer|NN|_ and|and|CC|_ acid|acid|NN|_ phenol-based|phenol-based|JJ|_ extraction|extraction|NN|_ method|method|NN|_ and|and|CC|_ isopropanol|isopropanol|NN|_ precipitation|precipitation|NN|_ .|.|.|_ Following|follow|VBG|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ treat|treat|VB|_ the|the|DT|_ samples|sample|NNS|_ as|as|IN|_ per|per|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ split|split|VBN|_ into|into|IN|_ five|five|CD|_ 20|20|CD|_ μL|μl|NN|_ aliquots|aliquot|NNS|_ and|and|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ were|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ each|each|DT|_ aliquot|aliquot|NN|_ .|.|.|_ Following|follow|VBG|_ DNase|dnase|NN|_ treatment|treatment|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ aliquots|aliquot|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ before|before|IN|_ purification|purification|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ measured|measure|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ while|while|IN|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Quant-iT|quant-it|JJ|_ RNA|rna|NN|_ Assay|assay|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ measured|measure|VBN|_ on|on|IN|_ a|a|DT|_ Qubit|Qubit|NNP|_ ®|®|NNP|_ 2.0|2.0|CD|_ fluorometer|fluorometer|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ at|at|IN|_ BGI|BGI|NNP|_ -LRB-|-lrb-|-LRB-|_ Shenzen|Shenzen|NNP|_ ,|,|,|_ China|China|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Aerobic|Aerobic|NNP|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 600|600|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ DM25|dm25|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ of|of|IN|_ 150|150|CD|_ RPM|rpm|NN|_ and|and|CC|_ inoculated|inoculate|VBN|_ with|with|IN|_ 1/100th|1/100th|JJ|_ volume|volume|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 9|9|CD|_ h|h|NN|_ while|while|IN|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 16|16|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Cultured|culture|VBN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ REL4536|rel4536|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stationary|stationary|JJ|_ phase|phase|NN|_
growth|growth|NN|_ environment|environment|NN|_ :|:|:|_ Aerobic|aerobic|JJ|_
Aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 600|600|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ DM25|dm25|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ of|of|IN|_ 150|150|CD|_ RPM|rpm|NN|_ and|and|CC|_ inoculated|inoculate|VBN|_ with|with|IN|_ 1/100th|1/100th|JJ|_ volume|volume|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 9|9|CD|_ h|h|NN|_ while|while|IN|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 16|16|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Cultured|culture|VBN|_ cells|cell|NNS|_
Christina|Christina|NNP|_ ,|,|,|_ ,|,|,|_ Moon|Moon|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium/low|medium/low|VB|_ sensitivity|sensitivity|NN|_ on|on|IN|_ Geneious|Geneious|NNP|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ gaps|gap|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 18|18|CD|_ ;|;|:|_ index|index|NN|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 13|13|CD|_ ;|;|:|_ words|word|NNS|_ repeated|repeat|VBN|_ more|more|JJR|_ than|than|IN|_ 12|12|CD|_ times|time|NNS|_ ignored|ignore|VBN|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ and|and|CC|_ maximum|maximum|JJ|_ ambiguity|ambiguity|NN|_ of|of|IN|_ 4|4|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ Wildtype|wildtype|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Rachel|Rachel|NNP|_ ,|,|,|_ ,|,|,|_ Krasich|Krasich|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium/low|medium/low|VB|_ sensitivity|sensitivity|NN|_ on|on|IN|_ Geneious|Geneious|NNP|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ gaps|gap|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 18|18|CD|_ ;|;|:|_ index|index|NN|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 13|13|CD|_ ;|;|:|_ words|word|NNS|_ repeated|repeat|VBN|_ more|more|JJR|_ than|than|IN|_ 12|12|CD|_ times|time|NNS|_ ignored|ignore|VBN|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ and|and|CC|_ maximum|maximum|JJ|_ ambiguity|ambiguity|NN|_ of|of|IN|_ 4|4|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ Wildtype|wildtype|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Rachel|Rachel|NNP|_ ,|,|,|_ ,|,|,|_ Krasich|Krasich|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium/low|medium/low|VB|_ sensitivity|sensitivity|NN|_ on|on|IN|_ Geneious|Geneious|NNP|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ gaps|gap|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 18|18|CD|_ ;|;|:|_ index|index|NN|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 13|13|CD|_ ;|;|:|_ words|word|NNS|_ repeated|repeat|VBN|_ more|more|JJR|_ than|than|IN|_ 12|12|CD|_ times|time|NNS|_ ignored|ignore|VBN|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ and|and|CC|_ maximum|maximum|JJ|_ ambiguity|ambiguity|NN|_ of|of|IN|_ 4|4|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ Wildtype|wildtype|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Rachel|Rachel|NNP|_ ,|,|,|_ ,|,|,|_ Krasich|Krasich|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium/low|medium/low|VB|_ sensitivity|sensitivity|NN|_ on|on|IN|_ Geneious|Geneious|NNP|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ gaps|gap|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 18|18|CD|_ ;|;|:|_ index|index|NN|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 13|13|CD|_ ;|;|:|_ words|word|NNS|_ repeated|repeat|VBN|_ more|more|JJR|_ than|than|IN|_ 12|12|CD|_ times|time|NNS|_ ignored|ignore|VBN|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ and|and|CC|_ maximum|maximum|JJ|_ ambiguity|ambiguity|NN|_ of|of|IN|_ 4|4|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ mfd|mfd|SYM|GEN -|-|:|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Rachel|Rachel|NNP|_ ,|,|,|_ ,|,|,|_ Krasich|Krasich|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium/low|medium/low|VB|_ sensitivity|sensitivity|NN|_ on|on|IN|_ Geneious|Geneious|NNP|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ gaps|gap|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 18|18|CD|_ ;|;|:|_ index|index|NN|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 13|13|CD|_ ;|;|:|_ words|word|NNS|_ repeated|repeat|VBN|_ more|more|JJR|_ than|than|IN|_ 12|12|CD|_ times|time|NNS|_ ignored|ignore|VBN|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ and|and|CC|_ maximum|maximum|JJ|_ ambiguity|ambiguity|NN|_ of|of|IN|_ 4|4|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ mfd|mfd|SYM|GEN -|-|:|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Rachel|Rachel|NNP|_ ,|,|,|_ ,|,|,|_ Krasich|Krasich|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium/low|medium/low|VB|_ sensitivity|sensitivity|NN|_ on|on|IN|_ Geneious|Geneious|NNP|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ gaps|gap|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 18|18|CD|_ ;|;|:|_ index|index|NN|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 13|13|CD|_ ;|;|:|_ words|word|NNS|_ repeated|repeat|VBN|_ more|more|JJR|_ than|than|IN|_ 12|12|CD|_ times|time|NNS|_ ignored|ignore|VBN|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ and|and|CC|_ maximum|maximum|JJ|_ ambiguity|ambiguity|NN|_ of|of|IN|_ 4|4|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ mfd|mfd|SYM|GEN -|-|:|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Rachel|Rachel|NNP|_ ,|,|,|_ ,|,|,|_ Krasich|Krasich|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium/low|medium/low|VB|_ sensitivity|sensitivity|NN|_ on|on|IN|_ Geneious|Geneious|NNP|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ gaps|gap|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 18|18|CD|_ ;|;|:|_ index|index|NN|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 13|13|CD|_ ;|;|:|_ words|word|NNS|_ repeated|repeat|VBN|_ more|more|JJR|_ than|than|IN|_ 12|12|CD|_ times|time|NNS|_ ignored|ignore|VBN|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ and|and|CC|_ maximum|maximum|JJ|_ ambiguity|ambiguity|NN|_ of|of|IN|_ 4|4|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ Wildtype|wildtype|NN|_ with|with|IN|_ vector|vector|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Rachel|Rachel|NNP|_ ,|,|,|_ ,|,|,|_ Krasich|Krasich|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium/low|medium/low|VB|_ sensitivity|sensitivity|NN|_ on|on|IN|_ Geneious|Geneious|NNP|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ gaps|gap|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 18|18|CD|_ ;|;|:|_ index|index|NN|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 13|13|CD|_ ;|;|:|_ words|word|NNS|_ repeated|repeat|VBN|_ more|more|JJR|_ than|than|IN|_ 12|12|CD|_ times|time|NNS|_ ignored|ignore|VBN|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ and|and|CC|_ maximum|maximum|JJ|_ ambiguity|ambiguity|NN|_ of|of|IN|_ 4|4|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ Wildtype|wildtype|NN|_ with|with|IN|_ vector|vector|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Rachel|Rachel|NNP|_ ,|,|,|_ ,|,|,|_ Krasich|Krasich|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium/low|medium/low|VB|_ sensitivity|sensitivity|NN|_ on|on|IN|_ Geneious|Geneious|NNP|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ gaps|gap|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 18|18|CD|_ ;|;|:|_ index|index|NN|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 13|13|CD|_ ;|;|:|_ words|word|NNS|_ repeated|repeat|VBN|_ more|more|JJR|_ than|than|IN|_ 12|12|CD|_ times|time|NNS|_ ignored|ignore|VBN|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ and|and|CC|_ maximum|maximum|JJ|_ ambiguity|ambiguity|NN|_ of|of|IN|_ 4|4|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ Mfd|mfd|NN|_ +|+|CC|_ +|+|CC|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Rachel|Rachel|NNP|_ ,|,|,|_ ,|,|,|_ Krasich|Krasich|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium/low|medium/low|VB|_ sensitivity|sensitivity|NN|_ on|on|IN|_ Geneious|Geneious|NNP|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ gaps|gap|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 18|18|CD|_ ;|;|:|_ index|index|NN|_ word|word|NN|_ length|length|NN|_ of|of|IN|_ 13|13|CD|_ ;|;|:|_ words|word|NNS|_ repeated|repeat|VBN|_ more|more|JJR|_ than|than|IN|_ 12|12|CD|_ times|time|NNS|_ ignored|ignore|VBN|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ maximum|maximum|NN|_ mismatches|mismatch|NNS|_ per|per|IN|_ read|read|NN|_ ;|;|:|_ and|and|CC|_ maximum|maximum|JJ|_ ambiguity|ambiguity|NN|_ of|of|IN|_ 4|4|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
genotype|genotype|NN|_ :|:|:|_ Mfd|mfd|NN|_ +|+|CC|_ +|+|CC|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Rachel|Rachel|NNP|_ ,|,|,|_ ,|,|,|_ Krasich|Krasich|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.1|17.1|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Space|Space|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 25|25|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.1|17.1|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.2|1.2|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Space|Space|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 25|25|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.2|1.2|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.3|17.3|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Space|Space|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 25|25|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.3|17.3|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.4|1.4|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Space|Space|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 25|25|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.4|1.4|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.5|17.5|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Space|Space|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 50|50|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.5|17.5|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.6|1.6|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Space|Space|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 50|50|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.6|1.6|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.6|17.6|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Space|Space|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 50|50|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.6|17.6|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
18.3|18.3|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Space|Space|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 75|75|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
18.3|18.3|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
2.4|2.4|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Space|Space|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 75|75|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
2.4|2.4|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.1|1.1|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 25|25|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.1|1.1|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.2|17.2|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 25|25|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.2|17.2|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.3|1.3|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 25|25|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.3|1.3|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.4|17.4|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 25|25|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.4|17.4|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.5|1.5|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 50|50|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.5|1.5|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.7|1.7|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 50|50|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
1.7|1.7|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.8|17.8|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 50|50|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
17.8|17.8|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 50|50|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
2.1|2.1|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 75|75|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
2.1|2.1|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
18.2|18.2|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 75|75|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
18.2|18.2|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
2.3|2.3|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 75|75|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
2.3|2.3|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Four|Four|NNP|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|be|VBZ|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
18.4|18.4|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug/ml|ug/ml|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 75|75|CD|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g/L|g/l|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ yielding|yield|VBG|_ 3.25|3.25|CD|_ mL|ml|NN|_ of|of|IN|_ a|a|DT|_ culture|culture|NN|_ with|with|IN|_ a|a|DT|_ starting|start|VBG|_ cell|cell|NN|_ concentration|concentration|NN|_ of|of|IN|_ 1.22|1.22|CD|_ e6|e6|NN|_ cell/mL|cell/ml|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
18.4|18.4|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug/mL|ug/ml|NN|_ in|in|IN|_ 25|25|CD|_ ug/mL|ug/ml|NN|_ steps|step|NNS|_ .|.|.|_ Thirty|thirty|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ -LRB-|-lrb-|-LRB-|_ ACROS|ACROS|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ .|.|.|_ No.|no.|NN|_ 41678|41678|CD|_ ,|,|,|_ New|New|NNP|_ Jersey|Jersey|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -75|-75|CD|_ C|c|NN|_ until|until|IN|_ return|return|NN|_ to|to|TO|_ Earth|Earth|NNP|_ for|for|IN|_ analyses|analysis|NNS|_ .|.|.|_
Luis|Luis|NNP|_ ,|,|,|_ ,|,|,|_ Zea|Zea|NNP|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC8739|atcc8739|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ CP000946|cp000946|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.2.5|2.2.5|CD|_ -RRB-|-rrb-|-RRB-|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
Detailed|detailed|JJ|_ parameters|parameter|NNS|_ for|for|IN|_ reads|read|VBZ|_ mapping|mapping|NN|_ :|:|:|_ bowtie2|bowtie2|NN|_ -|-|:|_ x|x|CC|_ ATCC8739|atcc8739|NN|_ -1|-1|CD|_ X|x|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ fq|fq|NN|_ -2|-2|CD|_ X|x|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ fq|fq|NN|_ --|--|:|_ no-mixed|no-mixed|JJ|_ -|-|:|_ p|p|NN|_ 2|2|CD|_ -|-|:|_ S|s|NN|_ X.sam|x.sam|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1938v1|asm1938v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ -LSB-|-lsb-|-LRB-|_ .|.|.|_ txt|txt|NN|_ -RSB-|-rsb-|-RRB-|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ the|the|DT|_ Trizol-Phenol-Chloroform|trizol-phenol-chloroform|NN|_ method|method|NN|_ .|.|.|_ An|a|DT|_ additional|additional|JJ|_ clean-up|clean-up|JJ|_ including|include|VBG|_ the|the|DT|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Single|single|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 15x100|15x100|CD|_ mm|mm|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 4|4|CD|_ ml|ml|NN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ .|.|.|_ 100|100|CD|_ μl|μl|NN|_ seed|seed|NN|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ a|a|DT|_ 100|100|CD|_ ml|ml|NN|_ flask|flask|NN|_ containing|contain|VBG|_ 10|10|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ 5|5|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
CAR005|car005|NN|_ strain|strain|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CAR005|car005|NN|_
Single|single|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 15x100|15x100|CD|_ mm|mm|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 4|4|CD|_ ml|ml|NN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ .|.|.|_ 100|100|CD|_ μl|μl|NN|_ seed|seed|NN|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ a|a|DT|_ 100|100|CD|_ ml|ml|NN|_ flask|flask|NN|_ containing|contain|VBG|_ 10|10|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ 5|5|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
CAR005|car005|NN|_ strain|strain|NN|_
feiyu|feiyu|NN|_ ,|,|,|_ ,|,|,|_ fan|fan|NN|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC8739|atcc8739|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ CP000946|cp000946|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.2.5|2.2.5|CD|_ -RRB-|-rrb-|-RRB-|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
Detailed|detailed|JJ|_ parameters|parameter|NNS|_ for|for|IN|_ reads|read|VBZ|_ mapping|mapping|NN|_ :|:|:|_ bowtie2|bowtie2|NN|_ -|-|:|_ x|x|CC|_ ATCC8739|atcc8739|NN|_ -1|-1|CD|_ X|x|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ fq|fq|NN|_ -2|-2|CD|_ X|x|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ fq|fq|NN|_ --|--|:|_ no-mixed|no-mixed|JJ|_ -|-|:|_ p|p|NN|_ 2|2|CD|_ -|-|:|_ S|s|NN|_ X.sam|x.sam|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1938v1|asm1938v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ -LSB-|-lsb-|-LRB-|_ .|.|.|_ txt|txt|NN|_ -RSB-|-rsb-|-RRB-|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ the|the|DT|_ Trizol-Phenol-Chloroform|trizol-phenol-chloroform|NN|_ method|method|NN|_ .|.|.|_ An|a|DT|_ additional|additional|JJ|_ clean-up|clean-up|JJ|_ including|include|VBG|_ the|the|DT|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Single|single|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 15x100|15x100|CD|_ mm|mm|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 4|4|CD|_ ml|ml|NN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ .|.|.|_ 100|100|CD|_ μl|μl|NN|_ seed|seed|NN|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ a|a|DT|_ 100|100|CD|_ ml|ml|NN|_ flask|flask|NN|_ containing|contain|VBG|_ 10|10|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ 5|5|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
G4H14|g4h14|NN|_ strain|strain|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ G4H14|g4h14|NN|_
Single|single|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 15x100|15x100|CD|_ mm|mm|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 4|4|CD|_ ml|ml|NN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ .|.|.|_ 100|100|CD|_ μl|μl|NN|_ seed|seed|NN|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ a|a|DT|_ 100|100|CD|_ ml|ml|NN|_ flask|flask|NN|_ containing|contain|VBG|_ 10|10|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ 5|5|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
G4H14|g4h14|NN|_ strain|strain|NN|_
feiyu|feiyu|NN|_ ,|,|,|_ ,|,|,|_ fan|fan|NN|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC8739|atcc8739|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ CP000946|cp000946|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.2.5|2.2.5|CD|_ -RRB-|-rrb-|-RRB-|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
Detailed|detailed|JJ|_ parameters|parameter|NNS|_ for|for|IN|_ reads|read|VBZ|_ mapping|mapping|NN|_ :|:|:|_ bowtie2|bowtie2|NN|_ -|-|:|_ x|x|CC|_ ATCC8739|atcc8739|NN|_ -1|-1|CD|_ X|x|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ fq|fq|NN|_ -2|-2|CD|_ X|x|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ fq|fq|NN|_ --|--|:|_ no-mixed|no-mixed|JJ|_ -|-|:|_ p|p|NN|_ 2|2|CD|_ -|-|:|_ S|s|NN|_ X.sam|x.sam|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1938v1|asm1938v1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ -LSB-|-lsb-|-LRB-|_ .|.|.|_ txt|txt|NN|_ -RSB-|-rsb-|-RRB-|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ the|the|DT|_ Trizol-Phenol-Chloroform|trizol-phenol-chloroform|NN|_ method|method|NN|_ .|.|.|_ An|a|DT|_ additional|additional|JJ|_ clean-up|clean-up|JJ|_ including|include|VBG|_ the|the|DT|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Single|single|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 15x100|15x100|CD|_ mm|mm|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 4|4|CD|_ ml|ml|NN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ .|.|.|_ 100|100|CD|_ μl|μl|NN|_ seed|seed|NN|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ a|a|DT|_ 100|100|CD|_ ml|ml|NN|_ flask|flask|NN|_ containing|contain|VBG|_ 10|10|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ 5|5|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
IspG1|ispg1|NN|_ strain|strain|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ IspG1|ispg1|NN|_
Single|single|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 15x100|15x100|CD|_ mm|mm|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 4|4|CD|_ ml|ml|NN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ .|.|.|_ 100|100|CD|_ μl|μl|NN|_ seed|seed|NN|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ a|a|DT|_ 100|100|CD|_ ml|ml|NN|_ flask|flask|NN|_ containing|contain|VBG|_ 10|10|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ 5|5|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
IspG1|ispg1|NN|_ strain|strain|NN|_
feiyu|feiyu|NN|_ ,|,|,|_ ,|,|,|_ fan|fan|NN|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC8739|atcc8739|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ CP000946|cp000946|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.2.5|2.2.5|CD|_ -RRB-|-rrb-|-RRB-|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
Detailed|detailed|JJ|_ parameters|parameter|NNS|_ for|for|IN|_ reads|read|VBZ|_ mapping|mapping|NN|_ :|:|:|_ bowtie2|bowtie2|NN|_ -|-|:|_ x|x|CC|_ ATCC8739|atcc8739|NN|_ -1|-1|CD|_ X|x|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ fq|fq|NN|_ -2|-2|CD|_ X|x|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ fq|fq|NN|_ --|--|:|_ no-mixed|no-mixed|JJ|_ -|-|:|_ p|p|NN|_ 2|2|CD|_ -|-|:|_ S|s|NN|_ X.sam|x.sam|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ATCC8739|atcc8739|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ the|the|DT|_ Trizol-Phenol-Chloroform|trizol-phenol-chloroform|NN|_ method|method|NN|_ .|.|.|_ An|a|DT|_ additional|additional|JJ|_ clean-up|clean-up|JJ|_ including|include|VBG|_ the|the|DT|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NZ-502|nz-502|NN|_ -LRB-|-lrb-|-LRB-|_ RpoB|rpob|NN|_ mutant|mutant|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ normal|normal|JJ|_ condtion|condtion|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ w/v|w/v|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_
feiyu|feiyu|NN|_ ,|,|,|_ ,|,|,|_ fan|fan|NN|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC8739|atcc8739|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ CP000946|cp000946|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.2.5|2.2.5|CD|_ -RRB-|-rrb-|-RRB-|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
Detailed|detailed|JJ|_ parameters|parameter|NNS|_ for|for|IN|_ reads|read|VBZ|_ mapping|mapping|NN|_ :|:|:|_ bowtie2|bowtie2|NN|_ -|-|:|_ x|x|CC|_ ATCC8739|atcc8739|NN|_ -1|-1|CD|_ X|x|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ fq|fq|NN|_ -2|-2|CD|_ X|x|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ fq|fq|NN|_ --|--|:|_ no-mixed|no-mixed|JJ|_ -|-|:|_ p|p|NN|_ 2|2|CD|_ -|-|:|_ S|s|NN|_ X.sam|x.sam|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ATCC8739|atcc8739|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ the|the|DT|_ Trizol-Phenol-Chloroform|trizol-phenol-chloroform|NN|_ method|method|NN|_ .|.|.|_ An|a|DT|_ additional|additional|JJ|_ clean-up|clean-up|JJ|_ including|include|VBG|_ the|the|DT|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NZ-502|nz-502|NN|_ -LRB-|-lrb-|-LRB-|_ RpoB|rpob|NN|_ mutant|mutant|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ condtion|condtion|NN|_ -LRB-|-lrb-|-LRB-|_ 12|12|CD|_ %|%|NN|_ w/v|w/v|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_
feiyu|feiyu|NN|_ ,|,|,|_ ,|,|,|_ fan|fan|NN|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC8739|atcc8739|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ CP000946|cp000946|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.2.5|2.2.5|CD|_ -RRB-|-rrb-|-RRB-|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
Detailed|detailed|JJ|_ parameters|parameter|NNS|_ for|for|IN|_ reads|read|VBZ|_ mapping|mapping|NN|_ :|:|:|_ bowtie2|bowtie2|NN|_ -|-|:|_ x|x|CC|_ ATCC8739|atcc8739|NN|_ -1|-1|CD|_ X|x|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ fq|fq|NN|_ -2|-2|CD|_ X|x|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ fq|fq|NN|_ --|--|:|_ no-mixed|no-mixed|JJ|_ -|-|:|_ p|p|NN|_ 2|2|CD|_ -|-|:|_ S|s|NN|_ X.sam|x.sam|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ATCC8739|atcc8739|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ the|the|DT|_ Trizol-Phenol-Chloroform|trizol-phenol-chloroform|NN|_ method|method|NN|_ .|.|.|_ An|a|DT|_ additional|additional|JJ|_ clean-up|clean-up|JJ|_ including|include|VBG|_ the|the|DT|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Suc-T110|suc-t110|NN|_ -LRB-|-lrb-|-LRB-|_ parental|parental|JJ|_ strain|strain|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ normal|normal|JJ|_ condtion|condtion|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ w/v|w/v|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_
feiyu|feiyu|NN|_ ,|,|,|_ ,|,|,|_ fan|fan|NN|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC8739|atcc8739|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ CP000946|cp000946|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.2.5|2.2.5|CD|_ -RRB-|-rrb-|-RRB-|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
Detailed|detailed|JJ|_ parameters|parameter|NNS|_ for|for|IN|_ reads|read|VBZ|_ mapping|mapping|NN|_ :|:|:|_ bowtie2|bowtie2|NN|_ -|-|:|_ x|x|CC|_ ATCC8739|atcc8739|NN|_ -1|-1|CD|_ X|x|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ fq|fq|NN|_ -2|-2|CD|_ X|x|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ fq|fq|NN|_ --|--|:|_ no-mixed|no-mixed|JJ|_ -|-|:|_ p|p|NN|_ 2|2|CD|_ -|-|:|_ S|s|NN|_ X.sam|x.sam|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ATCC8739|atcc8739|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ the|the|DT|_ Trizol-Phenol-Chloroform|trizol-phenol-chloroform|NN|_ method|method|NN|_ .|.|.|_ An|a|DT|_ additional|additional|JJ|_ clean-up|clean-up|JJ|_ including|include|VBG|_ the|the|DT|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Suc-T110|suc-t110|NN|_ -LRB-|-lrb-|-LRB-|_ parental|parental|JJ|_ strain|strain|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ condtion|condtion|NN|_ -LRB-|-lrb-|-LRB-|_ 12|12|CD|_ %|%|NN|_ w/v|w/v|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_
feiyu|feiyu|NN|_ ,|,|,|_ ,|,|,|_ fan|fan|NN|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Sean|Sean|NNP|_ ,|,|,|_ ,|,|,|_ Crosson|Crosson|NNP|_
RNA|rna|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ quality|quality|JJ|_ assessed|assess|VBN|_ and|and|CC|_ trimmed|trim|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ version|version|NN|_ 0.10.1|0.10.1|NN|_ -LRB-|-lrb-|-LRB-|_ www.bioinformatics.babraham.ac.uk/projects/fastqc/|www.bioinformatics.babraham.ac.uk/projects/fastqc/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ identification|identification|NN|_ of|of|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ to|to|TO|_ analyse|analyse|VB|_ the|the|DT|_ trimmed|trimmed|RBR|_ sequences|sequence|NNS|_ as|as|IN|_ a|a|DT|_ time|time|NN|_ course|course|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ 13-Feb-2011|13-feb-2011|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Tophat|Tophat|NNP|_ version|version|NN|_ 2.0.7|2.0.7|CD|_ .|.|.|_ Aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ assembled|assemble|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ version|version|NN|_ and|and|CC|_ merged|merge|VBD|_ using|use|VBG|_ cuffmerge|cuffmerge|NN|_ with|with|IN|_ an|a|DT|_ `|`|``|_ assemblies|assembly|NNS|_ '|'|POS|_ file|file|NN|_ containing|contain|VBG|_ the|the|DT|_ transcript.gtf|transcript.gtf|JJ|_ output|output|NN|_ files|file|NNS|_ from|from|IN|_ culfflinks|culfflink|NNS|_ .|.|.|_ Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ merged.gtf|merged.gtf|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ cuffmerge|cuffmerge|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 00091313-Feb-2011|00091313-feb-2011|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ each|each|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ isolated|isolate|VBN|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_ .|.|.|_ The|the|DT|_ 30|30|CD|_ mL|ml|NN|_ culture|culture|NN|_ was|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ three|three|CD|_ 15|15|CD|_ mL|ml|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ EtOH/Phenol|etoh/phenol|NN|_ stop|stop|VB|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ pH|ph|NN|_ 4.2|4.2|CD|_ -LSB-|-lsb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RSB-|-rsb-|-RRB-|_ in|in|IN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 4,000|4,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ suspended|suspend|VBN|_ in|in|IN|_ 800|800|CD|_ µL|µl|NN|_ TE|TE|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ .|.|.|_ SDS|sds|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ µL|µl|NN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ samples|sample|NNS|_ mixed|mix|VBN|_ by|by|IN|_ inversion|inversion|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 88|88|CD|_ µL|µl|NN|_ 1|1|CD|_ M|m|NN|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ -LRB-|-lrb-|-LRB-|_ 1mL|1ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.2|4.2|CD|_ ,|,|,|_ 65|65|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 6|6|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ solution|solution|NN|_ was|be|VBD|_ separated|separate|VBN|_ into|into|IN|_ layers|layer|NNS|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ upper|upper|JJ|_ aqueous|aqueous|JJ|_ RNA|rna|NN|_ containing|contain|VBG|_ layer|layer|NN|_ removed|remove|VBD|_ and|and|CC|_ transferred|transfer|VBD|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ by|by|IN|_ three|three|CD|_ extractions|extraction|NNS|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ CHCl3|chcl3|NN|_ :|:|:|_ IAA|iaa|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ precipitated|precipitated|JJ|_ -LRB-|-lrb-|-LRB-|_ -80|-80|CD|_ °C|°c|NN|_ ,|,|,|_ O/N|o/n|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1/10|1/10|CD|_ volume|volume|NN|_ of|of|IN|_ 3M|3M|NNP|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2|2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice|ice|NN|_ cold|cold|JJ|_ 100|100|CD|_ %|%|NN|_ EtOH|etoh|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ supernatant|supernatant|JJ|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ 75|75|CD|_ %|%|NN|_ cold|cold|JJ|_ EtOH|etoh|NN|_ -LRB-|-lrb-|-LRB-|_ made|make|VBN|_ with|with|IN|_ DEPC-treated|depc-treated|JJ|_ water|water|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ air|air|NN|_ dried|dry|VBD|_ before|before|IN|_ suspension|suspension|NN|_ in|in|IN|_ 80|80|CD|_ µL|µl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ 10|10|CD|_ X|x|NN|_ Turbo|Turbo|NNP|_ DNAse|dnase|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ RNA|rna|NN|_ solution|solution|NN|_ .|.|.|_ 1|1|CD|_ µL|µl|NN|_ of|of|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ solution|solution|NN|_ ,|,|,|_ which|which|WDT|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ DNase|dnase|NN|_ Inactivation|inactivation|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ occasional|occasional|JJ|_ mixing|mix|VBG|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ microfuge|microfuge|NN|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ tested|test|VBN|_ using|use|VBG|_ the|the|DT|_ the|the|DT|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ analysed|analyse|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ each|each|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ isolated|isolate|VBN|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_ .|.|.|_ The|the|DT|_ 30|30|CD|_ mL|ml|NN|_ culture|culture|NN|_ was|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ three|three|CD|_ 15|15|CD|_ mL|ml|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ EtOH/Phenol|etoh/phenol|NN|_ stop|stop|VB|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ pH|ph|NN|_ 4.2|4.2|CD|_ -LSB-|-lsb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RSB-|-rsb-|-RRB-|_ in|in|IN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 4,000|4,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ suspended|suspend|VBN|_ in|in|IN|_ 800|800|CD|_ µL|µl|NN|_ TE|TE|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ .|.|.|_ SDS|sds|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ µL|µl|NN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ samples|sample|NNS|_ mixed|mix|VBN|_ by|by|IN|_ inversion|inversion|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 88|88|CD|_ µL|µl|NN|_ 1|1|CD|_ M|m|NN|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ -LRB-|-lrb-|-LRB-|_ 1mL|1ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.2|4.2|CD|_ ,|,|,|_ 65|65|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 6|6|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ solution|solution|NN|_ was|be|VBD|_ separated|separate|VBN|_ into|into|IN|_ layers|layer|NNS|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ upper|upper|JJ|_ aqueous|aqueous|JJ|_ RNA|rna|NN|_ containing|contain|VBG|_ layer|layer|NN|_ removed|remove|VBD|_ and|and|CC|_ transferred|transfer|VBD|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ by|by|IN|_ three|three|CD|_ extractions|extraction|NNS|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ CHCl3|chcl3|NN|_ :|:|:|_ IAA|iaa|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ precipitated|precipitated|JJ|_ -LRB-|-lrb-|-LRB-|_ -80|-80|CD|_ °C|°c|NN|_ ,|,|,|_ O/N|o/n|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1/10|1/10|CD|_ volume|volume|NN|_ of|of|IN|_ 3M|3M|NNP|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2|2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice|ice|NN|_ cold|cold|JJ|_ 100|100|CD|_ %|%|NN|_ EtOH|etoh|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ supernatant|supernatant|JJ|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ 75|75|CD|_ %|%|NN|_ cold|cold|JJ|_ EtOH|etoh|NN|_ -LRB-|-lrb-|-LRB-|_ made|make|VBN|_ with|with|IN|_ DEPC-treated|depc-treated|JJ|_ water|water|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ air|air|NN|_ dried|dry|VBD|_ before|before|IN|_ suspension|suspension|NN|_ in|in|IN|_ 80|80|CD|_ µL|µl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ 10|10|CD|_ X|x|NN|_ Turbo|Turbo|NNP|_ DNAse|dnase|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ RNA|rna|NN|_ solution|solution|NN|_ .|.|.|_ 1|1|CD|_ µL|µl|NN|_ of|of|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ solution|solution|NN|_ ,|,|,|_ which|which|WDT|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ DNase|dnase|NN|_ Inactivation|inactivation|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ occasional|occasional|JJ|_ mixing|mix|VBG|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ microfuge|microfuge|NN|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ tested|test|VBN|_ using|use|VBG|_ the|the|DT|_ the|the|DT|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ analysed|analyse|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
200|200|CD|_ bp|bp|NN|_ insert|insert|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depletion|depletion|NN|_
Synchronization|synchronization|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ passaging|passaging|NN|_ cells|cell|NNS|_ through|through|IN|_ one|one|CD|_ or|or|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase according|accord|VBG|_ to|to|TO|_ Cutler|Cutler|NNP|_ and|and|CC|_ Evans|Evans|NNP|_ 1966|1966|CD|_ .|.|.|_ Briefly|briefly|RB|_ :|:|:|_ Individual|individual|JJ|_ colonies|colony|NNS|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ plate|plate|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 24|24|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ O/N|o/n|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|_ media|media|NNS|_ was|be|VBD|_ inoculated|inoculate|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ early-logarithmic|early-logarithmic|JJ|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ maintained|maintain|VBN|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ approximately|approximately|RB|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ An|a|DT|_ appropriate|appropriate|JJ|_ amount|amount|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ pre-warmed|pre-warmed|JJ|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ media|media|NNS|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ approximate|approximate|JJ|_ 7-fold|7-fold|JJ|_ dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Released|release|VBN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ harvested|harvest|VBN|_ -LRB-|-lrb-|-LRB-|_ time|time|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ or|or|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ GCC|gcc|NN|_ and|and|CC|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ also|also|RB|_ taken|take|VBN|_ for|for|IN|_ FACS|facs|NN|_ analysis|analysis|NN|_ and|and|CC|_ fluorescence|fluorescence|NN|_ microscopy|microscopy|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Stationary|stationary|JJ|_ phase|phase|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ sampled|sample|VBN|_ at|at|IN|_ times|time|NNS|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hour|hour|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hours|hour|NNS|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_
RNA-Seq|rna-seq|NN|_
time|time|NN|_ post|post|NN|_ release|release|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ immediately|immediately|RB|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ Stationary|stationary|JJ|_ phase|phase|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ Replicate|replicate|VB|_ 1|1|CD|_
Synchronization|synchronization|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ passaging|passaging|NN|_ cells|cell|NNS|_ through|through|IN|_ one|one|CD|_ or|or|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase according|accord|VBG|_ to|to|TO|_ Cutler|Cutler|NNP|_ and|and|CC|_ Evans|Evans|NNP|_ 1966|1966|CD|_ .|.|.|_ Briefly|briefly|RB|_ :|:|:|_ Individual|individual|JJ|_ colonies|colony|NNS|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ plate|plate|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 24|24|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ O/N|o/n|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|_ media|media|NNS|_ was|be|VBD|_ inoculated|inoculate|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ early-logarithmic|early-logarithmic|JJ|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ maintained|maintain|VBN|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ approximately|approximately|RB|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ An|a|DT|_ appropriate|appropriate|JJ|_ amount|amount|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ pre-warmed|pre-warmed|JJ|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ media|media|NNS|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ approximate|approximate|JJ|_ 7-fold|7-fold|JJ|_ dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Released|release|VBN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ harvested|harvest|VBN|_ -LRB-|-lrb-|-LRB-|_ time|time|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ or|or|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ GCC|gcc|NN|_ and|and|CC|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ also|also|RB|_ taken|take|VBN|_ for|for|IN|_ FACS|facs|NN|_ analysis|analysis|NN|_ and|and|CC|_ fluorescence|fluorescence|NN|_ microscopy|microscopy|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Stationary|stationary|JJ|_ phase|phase|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ sampled|sample|VBN|_ at|at|IN|_ times|time|NNS|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hour|hour|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hours|hour|NNS|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_
Justin|Justin|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ O|o|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Sullivan|Sullivan|NNP|_
RNA|rna|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ quality|quality|JJ|_ assessed|assess|VBN|_ and|and|CC|_ trimmed|trim|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ version|version|NN|_ 0.10.1|0.10.1|NN|_ -LRB-|-lrb-|-LRB-|_ www.bioinformatics.babraham.ac.uk/projects/fastqc/|www.bioinformatics.babraham.ac.uk/projects/fastqc/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ identification|identification|NN|_ of|of|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ to|to|TO|_ analyse|analyse|VB|_ the|the|DT|_ trimmed|trimmed|RBR|_ sequences|sequence|NNS|_ as|as|IN|_ a|a|DT|_ time|time|NN|_ course|course|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ 13-Feb-2011|13-feb-2011|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Tophat|Tophat|NNP|_ version|version|NN|_ 2.0.7|2.0.7|CD|_ .|.|.|_ Aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ assembled|assemble|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ version|version|NN|_ and|and|CC|_ merged|merge|VBD|_ using|use|VBG|_ cuffmerge|cuffmerge|NN|_ with|with|IN|_ an|a|DT|_ `|`|``|_ assemblies|assembly|NNS|_ '|'|POS|_ file|file|NN|_ containing|contain|VBG|_ the|the|DT|_ transcript.gtf|transcript.gtf|JJ|_ output|output|NN|_ files|file|NNS|_ from|from|IN|_ culfflinks|culfflink|NNS|_ .|.|.|_ Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ merged.gtf|merged.gtf|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ cuffmerge|cuffmerge|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 00091313-Feb-2011|00091313-feb-2011|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ each|each|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ isolated|isolate|VBN|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_ .|.|.|_ The|the|DT|_ 30|30|CD|_ mL|ml|NN|_ culture|culture|NN|_ was|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ three|three|CD|_ 15|15|CD|_ mL|ml|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ EtOH/Phenol|etoh/phenol|NN|_ stop|stop|VB|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ pH|ph|NN|_ 4.2|4.2|CD|_ -LSB-|-lsb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RSB-|-rsb-|-RRB-|_ in|in|IN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 4,000|4,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ suspended|suspend|VBN|_ in|in|IN|_ 800|800|CD|_ µL|µl|NN|_ TE|TE|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ .|.|.|_ SDS|sds|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ µL|µl|NN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ samples|sample|NNS|_ mixed|mix|VBN|_ by|by|IN|_ inversion|inversion|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 88|88|CD|_ µL|µl|NN|_ 1|1|CD|_ M|m|NN|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ -LRB-|-lrb-|-LRB-|_ 1mL|1ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.2|4.2|CD|_ ,|,|,|_ 65|65|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 6|6|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ solution|solution|NN|_ was|be|VBD|_ separated|separate|VBN|_ into|into|IN|_ layers|layer|NNS|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ upper|upper|JJ|_ aqueous|aqueous|JJ|_ RNA|rna|NN|_ containing|contain|VBG|_ layer|layer|NN|_ removed|remove|VBD|_ and|and|CC|_ transferred|transfer|VBD|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ by|by|IN|_ three|three|CD|_ extractions|extraction|NNS|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ CHCl3|chcl3|NN|_ :|:|:|_ IAA|iaa|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ precipitated|precipitated|JJ|_ -LRB-|-lrb-|-LRB-|_ -80|-80|CD|_ °C|°c|NN|_ ,|,|,|_ O/N|o/n|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1/10|1/10|CD|_ volume|volume|NN|_ of|of|IN|_ 3M|3M|NNP|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2|2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice|ice|NN|_ cold|cold|JJ|_ 100|100|CD|_ %|%|NN|_ EtOH|etoh|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ supernatant|supernatant|JJ|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ 75|75|CD|_ %|%|NN|_ cold|cold|JJ|_ EtOH|etoh|NN|_ -LRB-|-lrb-|-LRB-|_ made|make|VBN|_ with|with|IN|_ DEPC-treated|depc-treated|JJ|_ water|water|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ air|air|NN|_ dried|dry|VBD|_ before|before|IN|_ suspension|suspension|NN|_ in|in|IN|_ 80|80|CD|_ µL|µl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ 10|10|CD|_ X|x|NN|_ Turbo|Turbo|NNP|_ DNAse|dnase|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ RNA|rna|NN|_ solution|solution|NN|_ .|.|.|_ 1|1|CD|_ µL|µl|NN|_ of|of|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ solution|solution|NN|_ ,|,|,|_ which|which|WDT|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ DNase|dnase|NN|_ Inactivation|inactivation|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ occasional|occasional|JJ|_ mixing|mix|VBG|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ microfuge|microfuge|NN|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ tested|test|VBN|_ using|use|VBG|_ the|the|DT|_ the|the|DT|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ analysed|analyse|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ each|each|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ isolated|isolate|VBN|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_ .|.|.|_ The|the|DT|_ 30|30|CD|_ mL|ml|NN|_ culture|culture|NN|_ was|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ three|three|CD|_ 15|15|CD|_ mL|ml|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ EtOH/Phenol|etoh/phenol|NN|_ stop|stop|VB|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ pH|ph|NN|_ 4.2|4.2|CD|_ -LSB-|-lsb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RSB-|-rsb-|-RRB-|_ in|in|IN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 4,000|4,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ suspended|suspend|VBN|_ in|in|IN|_ 800|800|CD|_ µL|µl|NN|_ TE|TE|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ .|.|.|_ SDS|sds|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ µL|µl|NN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ samples|sample|NNS|_ mixed|mix|VBN|_ by|by|IN|_ inversion|inversion|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 88|88|CD|_ µL|µl|NN|_ 1|1|CD|_ M|m|NN|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ -LRB-|-lrb-|-LRB-|_ 1mL|1ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.2|4.2|CD|_ ,|,|,|_ 65|65|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 6|6|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ solution|solution|NN|_ was|be|VBD|_ separated|separate|VBN|_ into|into|IN|_ layers|layer|NNS|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ upper|upper|JJ|_ aqueous|aqueous|JJ|_ RNA|rna|NN|_ containing|contain|VBG|_ layer|layer|NN|_ removed|remove|VBD|_ and|and|CC|_ transferred|transfer|VBD|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ by|by|IN|_ three|three|CD|_ extractions|extraction|NNS|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ CHCl3|chcl3|NN|_ :|:|:|_ IAA|iaa|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ precipitated|precipitated|JJ|_ -LRB-|-lrb-|-LRB-|_ -80|-80|CD|_ °C|°c|NN|_ ,|,|,|_ O/N|o/n|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1/10|1/10|CD|_ volume|volume|NN|_ of|of|IN|_ 3M|3M|NNP|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2|2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice|ice|NN|_ cold|cold|JJ|_ 100|100|CD|_ %|%|NN|_ EtOH|etoh|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ supernatant|supernatant|JJ|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ 75|75|CD|_ %|%|NN|_ cold|cold|JJ|_ EtOH|etoh|NN|_ -LRB-|-lrb-|-LRB-|_ made|make|VBN|_ with|with|IN|_ DEPC-treated|depc-treated|JJ|_ water|water|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ air|air|NN|_ dried|dry|VBD|_ before|before|IN|_ suspension|suspension|NN|_ in|in|IN|_ 80|80|CD|_ µL|µl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ 10|10|CD|_ X|x|NN|_ Turbo|Turbo|NNP|_ DNAse|dnase|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ RNA|rna|NN|_ solution|solution|NN|_ .|.|.|_ 1|1|CD|_ µL|µl|NN|_ of|of|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ solution|solution|NN|_ ,|,|,|_ which|which|WDT|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ DNase|dnase|NN|_ Inactivation|inactivation|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ occasional|occasional|JJ|_ mixing|mix|VBG|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ microfuge|microfuge|NN|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ tested|test|VBN|_ using|use|VBG|_ the|the|DT|_ the|the|DT|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ analysed|analyse|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
200|200|CD|_ bp|bp|NN|_ insert|insert|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depletion|depletion|NN|_
Synchronization|synchronization|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ passaging|passaging|NN|_ cells|cell|NNS|_ through|through|IN|_ one|one|CD|_ or|or|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase according|accord|VBG|_ to|to|TO|_ Cutler|Cutler|NNP|_ and|and|CC|_ Evans|Evans|NNP|_ 1966|1966|CD|_ .|.|.|_ Briefly|briefly|RB|_ :|:|:|_ Individual|individual|JJ|_ colonies|colony|NNS|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ plate|plate|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 24|24|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ O/N|o/n|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|_ media|media|NNS|_ was|be|VBD|_ inoculated|inoculate|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ early-logarithmic|early-logarithmic|JJ|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ maintained|maintain|VBN|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ approximately|approximately|RB|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ An|a|DT|_ appropriate|appropriate|JJ|_ amount|amount|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ pre-warmed|pre-warmed|JJ|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ media|media|NNS|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ approximate|approximate|JJ|_ 7-fold|7-fold|JJ|_ dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Released|release|VBN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ harvested|harvest|VBN|_ -LRB-|-lrb-|-LRB-|_ time|time|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ or|or|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ GCC|gcc|NN|_ and|and|CC|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ also|also|RB|_ taken|take|VBN|_ for|for|IN|_ FACS|facs|NN|_ analysis|analysis|NN|_ and|and|CC|_ fluorescence|fluorescence|NN|_ microscopy|microscopy|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Growing|grow|VBG|_ t|t|NN|_ =|=|JJ|_ 1|1|CD|_ hour|hour|NN|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ sampled|sample|VBN|_ at|at|IN|_ times|time|NNS|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hour|hour|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hours|hour|NNS|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_
RNA-Seq|rna-seq|NN|_
time|time|NN|_ post|post|NN|_ release|release|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ 1|1|CD|_ hour|hour|NN|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ Stationary|stationary|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ Replicate|replicate|VB|_ 1|1|CD|_
Synchronization|synchronization|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ passaging|passaging|NN|_ cells|cell|NNS|_ through|through|IN|_ one|one|CD|_ or|or|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase according|accord|VBG|_ to|to|TO|_ Cutler|Cutler|NNP|_ and|and|CC|_ Evans|Evans|NNP|_ 1966|1966|CD|_ .|.|.|_ Briefly|briefly|RB|_ :|:|:|_ Individual|individual|JJ|_ colonies|colony|NNS|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ plate|plate|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 24|24|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ O/N|o/n|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|_ media|media|NNS|_ was|be|VBD|_ inoculated|inoculate|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ early-logarithmic|early-logarithmic|JJ|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ maintained|maintain|VBN|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ approximately|approximately|RB|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ An|a|DT|_ appropriate|appropriate|JJ|_ amount|amount|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ pre-warmed|pre-warmed|JJ|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ media|media|NNS|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ approximate|approximate|JJ|_ 7-fold|7-fold|JJ|_ dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Released|release|VBN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ harvested|harvest|VBN|_ -LRB-|-lrb-|-LRB-|_ time|time|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ or|or|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ GCC|gcc|NN|_ and|and|CC|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ also|also|RB|_ taken|take|VBN|_ for|for|IN|_ FACS|facs|NN|_ analysis|analysis|NN|_ and|and|CC|_ fluorescence|fluorescence|NN|_ microscopy|microscopy|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Growing|grow|VBG|_ t|t|NN|_ =|=|JJ|_ 1|1|CD|_ hour|hour|NN|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ sampled|sample|VBN|_ at|at|IN|_ times|time|NNS|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hour|hour|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hours|hour|NNS|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_
Justin|Justin|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ O|o|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Sullivan|Sullivan|NNP|_
RNA|rna|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ quality|quality|JJ|_ assessed|assess|VBN|_ and|and|CC|_ trimmed|trim|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ version|version|NN|_ 0.10.1|0.10.1|NN|_ -LRB-|-lrb-|-LRB-|_ www.bioinformatics.babraham.ac.uk/projects/fastqc/|www.bioinformatics.babraham.ac.uk/projects/fastqc/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ identification|identification|NN|_ of|of|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ to|to|TO|_ analyse|analyse|VB|_ the|the|DT|_ trimmed|trimmed|RBR|_ sequences|sequence|NNS|_ as|as|IN|_ a|a|DT|_ time|time|NN|_ course|course|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ 13-Feb-2011|13-feb-2011|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Tophat|Tophat|NNP|_ version|version|NN|_ 2.0.7|2.0.7|CD|_ .|.|.|_ Aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ assembled|assemble|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ version|version|NN|_ and|and|CC|_ merged|merge|VBD|_ using|use|VBG|_ cuffmerge|cuffmerge|NN|_ with|with|IN|_ an|a|DT|_ `|`|``|_ assemblies|assembly|NNS|_ '|'|POS|_ file|file|NN|_ containing|contain|VBG|_ the|the|DT|_ transcript.gtf|transcript.gtf|JJ|_ output|output|NN|_ files|file|NNS|_ from|from|IN|_ culfflinks|culfflink|NNS|_ .|.|.|_ Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ merged.gtf|merged.gtf|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ cuffmerge|cuffmerge|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 00091313-Feb-2011|00091313-feb-2011|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ each|each|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ isolated|isolate|VBN|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_ .|.|.|_ The|the|DT|_ 30|30|CD|_ mL|ml|NN|_ culture|culture|NN|_ was|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ three|three|CD|_ 15|15|CD|_ mL|ml|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ EtOH/Phenol|etoh/phenol|NN|_ stop|stop|VB|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ pH|ph|NN|_ 4.2|4.2|CD|_ -LSB-|-lsb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RSB-|-rsb-|-RRB-|_ in|in|IN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 4,000|4,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ suspended|suspend|VBN|_ in|in|IN|_ 800|800|CD|_ µL|µl|NN|_ TE|TE|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ .|.|.|_ SDS|sds|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ µL|µl|NN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ samples|sample|NNS|_ mixed|mix|VBN|_ by|by|IN|_ inversion|inversion|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 88|88|CD|_ µL|µl|NN|_ 1|1|CD|_ M|m|NN|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ -LRB-|-lrb-|-LRB-|_ 1mL|1ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.2|4.2|CD|_ ,|,|,|_ 65|65|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 6|6|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ solution|solution|NN|_ was|be|VBD|_ separated|separate|VBN|_ into|into|IN|_ layers|layer|NNS|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ upper|upper|JJ|_ aqueous|aqueous|JJ|_ RNA|rna|NN|_ containing|contain|VBG|_ layer|layer|NN|_ removed|remove|VBD|_ and|and|CC|_ transferred|transfer|VBD|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ by|by|IN|_ three|three|CD|_ extractions|extraction|NNS|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ CHCl3|chcl3|NN|_ :|:|:|_ IAA|iaa|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ precipitated|precipitated|JJ|_ -LRB-|-lrb-|-LRB-|_ -80|-80|CD|_ °C|°c|NN|_ ,|,|,|_ O/N|o/n|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1/10|1/10|CD|_ volume|volume|NN|_ of|of|IN|_ 3M|3M|NNP|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2|2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice|ice|NN|_ cold|cold|JJ|_ 100|100|CD|_ %|%|NN|_ EtOH|etoh|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ supernatant|supernatant|JJ|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ 75|75|CD|_ %|%|NN|_ cold|cold|JJ|_ EtOH|etoh|NN|_ -LRB-|-lrb-|-LRB-|_ made|make|VBN|_ with|with|IN|_ DEPC-treated|depc-treated|JJ|_ water|water|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ air|air|NN|_ dried|dry|VBD|_ before|before|IN|_ suspension|suspension|NN|_ in|in|IN|_ 80|80|CD|_ µL|µl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ 10|10|CD|_ X|x|NN|_ Turbo|Turbo|NNP|_ DNAse|dnase|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ RNA|rna|NN|_ solution|solution|NN|_ .|.|.|_ 1|1|CD|_ µL|µl|NN|_ of|of|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ solution|solution|NN|_ ,|,|,|_ which|which|WDT|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ DNase|dnase|NN|_ Inactivation|inactivation|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ occasional|occasional|JJ|_ mixing|mix|VBG|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ microfuge|microfuge|NN|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ tested|test|VBN|_ using|use|VBG|_ the|the|DT|_ the|the|DT|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ analysed|analyse|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ each|each|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ isolated|isolate|VBN|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_ .|.|.|_ The|the|DT|_ 30|30|CD|_ mL|ml|NN|_ culture|culture|NN|_ was|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ three|three|CD|_ 15|15|CD|_ mL|ml|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ EtOH/Phenol|etoh/phenol|NN|_ stop|stop|VB|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ pH|ph|NN|_ 4.2|4.2|CD|_ -LSB-|-lsb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RSB-|-rsb-|-RRB-|_ in|in|IN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 4,000|4,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ suspended|suspend|VBN|_ in|in|IN|_ 800|800|CD|_ µL|µl|NN|_ TE|TE|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ .|.|.|_ SDS|sds|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ µL|µl|NN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ samples|sample|NNS|_ mixed|mix|VBN|_ by|by|IN|_ inversion|inversion|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 88|88|CD|_ µL|µl|NN|_ 1|1|CD|_ M|m|NN|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ -LRB-|-lrb-|-LRB-|_ 1mL|1ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.2|4.2|CD|_ ,|,|,|_ 65|65|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 6|6|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ solution|solution|NN|_ was|be|VBD|_ separated|separate|VBN|_ into|into|IN|_ layers|layer|NNS|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ upper|upper|JJ|_ aqueous|aqueous|JJ|_ RNA|rna|NN|_ containing|contain|VBG|_ layer|layer|NN|_ removed|remove|VBD|_ and|and|CC|_ transferred|transfer|VBD|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ by|by|IN|_ three|three|CD|_ extractions|extraction|NNS|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ CHCl3|chcl3|NN|_ :|:|:|_ IAA|iaa|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ precipitated|precipitated|JJ|_ -LRB-|-lrb-|-LRB-|_ -80|-80|CD|_ °C|°c|NN|_ ,|,|,|_ O/N|o/n|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1/10|1/10|CD|_ volume|volume|NN|_ of|of|IN|_ 3M|3M|NNP|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2|2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice|ice|NN|_ cold|cold|JJ|_ 100|100|CD|_ %|%|NN|_ EtOH|etoh|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ supernatant|supernatant|JJ|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ 75|75|CD|_ %|%|NN|_ cold|cold|JJ|_ EtOH|etoh|NN|_ -LRB-|-lrb-|-LRB-|_ made|make|VBN|_ with|with|IN|_ DEPC-treated|depc-treated|JJ|_ water|water|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ air|air|NN|_ dried|dry|VBD|_ before|before|IN|_ suspension|suspension|NN|_ in|in|IN|_ 80|80|CD|_ µL|µl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ 10|10|CD|_ X|x|NN|_ Turbo|Turbo|NNP|_ DNAse|dnase|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ RNA|rna|NN|_ solution|solution|NN|_ .|.|.|_ 1|1|CD|_ µL|µl|NN|_ of|of|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ solution|solution|NN|_ ,|,|,|_ which|which|WDT|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ DNase|dnase|NN|_ Inactivation|inactivation|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ occasional|occasional|JJ|_ mixing|mix|VBG|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ microfuge|microfuge|NN|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ tested|test|VBN|_ using|use|VBG|_ the|the|DT|_ the|the|DT|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ analysed|analyse|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
200|200|CD|_ bp|bp|NN|_ insert|insert|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depletion|depletion|NN|_
Synchronization|synchronization|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ passaging|passaging|NN|_ cells|cell|NNS|_ through|through|IN|_ one|one|CD|_ or|or|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase according|accord|VBG|_ to|to|TO|_ Cutler|Cutler|NNP|_ and|and|CC|_ Evans|Evans|NNP|_ 1966|1966|CD|_ .|.|.|_ Briefly|briefly|RB|_ :|:|:|_ Individual|individual|JJ|_ colonies|colony|NNS|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ plate|plate|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 24|24|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ O/N|o/n|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|_ media|media|NNS|_ was|be|VBD|_ inoculated|inoculate|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ early-logarithmic|early-logarithmic|JJ|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ maintained|maintain|VBN|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ approximately|approximately|RB|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ An|a|DT|_ appropriate|appropriate|JJ|_ amount|amount|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ pre-warmed|pre-warmed|JJ|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ media|media|NNS|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ approximate|approximate|JJ|_ 7-fold|7-fold|JJ|_ dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Released|release|VBN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ harvested|harvest|VBN|_ -LRB-|-lrb-|-LRB-|_ time|time|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ or|or|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ GCC|gcc|NN|_ and|and|CC|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ also|also|RB|_ taken|take|VBN|_ for|for|IN|_ FACS|facs|NN|_ analysis|analysis|NN|_ and|and|CC|_ fluorescence|fluorescence|NN|_ microscopy|microscopy|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Dividing|divide|VBG|_ t|t|NN|_ =|=|JJ|_ 2|2|CD|_ hours|hour|NNS|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ sampled|sample|VBN|_ at|at|IN|_ times|time|NNS|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hour|hour|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hours|hour|NNS|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_
RNA-Seq|rna-seq|NN|_
time|time|NN|_ post|post|NN|_ release|release|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ 2|2|CD|_ hour2|hour2|NN|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ Stationary|stationary|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ Replicate|replicate|VB|_ 1|1|CD|_
Synchronization|synchronization|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ passaging|passaging|NN|_ cells|cell|NNS|_ through|through|IN|_ one|one|CD|_ or|or|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase according|accord|VBG|_ to|to|TO|_ Cutler|Cutler|NNP|_ and|and|CC|_ Evans|Evans|NNP|_ 1966|1966|CD|_ .|.|.|_ Briefly|briefly|RB|_ :|:|:|_ Individual|individual|JJ|_ colonies|colony|NNS|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ plate|plate|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 24|24|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ O/N|o/n|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|_ media|media|NNS|_ was|be|VBD|_ inoculated|inoculate|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ early-logarithmic|early-logarithmic|JJ|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ maintained|maintain|VBN|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ approximately|approximately|RB|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ An|a|DT|_ appropriate|appropriate|JJ|_ amount|amount|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ pre-warmed|pre-warmed|JJ|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ media|media|NNS|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ approximate|approximate|JJ|_ 7-fold|7-fold|JJ|_ dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Released|release|VBN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ harvested|harvest|VBN|_ -LRB-|-lrb-|-LRB-|_ time|time|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ or|or|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ GCC|gcc|NN|_ and|and|CC|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ also|also|RB|_ taken|take|VBN|_ for|for|IN|_ FACS|facs|NN|_ analysis|analysis|NN|_ and|and|CC|_ fluorescence|fluorescence|NN|_ microscopy|microscopy|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Dividing|divide|VBG|_ t|t|NN|_ =|=|JJ|_ 2|2|CD|_ hours|hour|NNS|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ sampled|sample|VBN|_ at|at|IN|_ times|time|NNS|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hour|hour|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hours|hour|NNS|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_
Justin|Justin|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ O|o|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Sullivan|Sullivan|NNP|_
RNA|rna|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ quality|quality|JJ|_ assessed|assess|VBN|_ and|and|CC|_ trimmed|trim|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ version|version|NN|_ 0.10.1|0.10.1|NN|_ -LRB-|-lrb-|-LRB-|_ www.bioinformatics.babraham.ac.uk/projects/fastqc/|www.bioinformatics.babraham.ac.uk/projects/fastqc/|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ identification|identification|NN|_ of|of|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ to|to|TO|_ analyse|analyse|VB|_ the|the|DT|_ trimmed|trimmed|RBR|_ sequences|sequence|NNS|_ as|as|IN|_ a|a|DT|_ time|time|NN|_ course|course|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ 13-Feb-2011|13-feb-2011|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Tophat|Tophat|NNP|_ version|version|NN|_ 2.0.7|2.0.7|CD|_ .|.|.|_ Aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ assembled|assemble|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ version|version|NN|_ and|and|CC|_ merged|merge|VBD|_ using|use|VBG|_ cuffmerge|cuffmerge|NN|_ with|with|IN|_ an|a|DT|_ `|`|``|_ assemblies|assembly|NNS|_ '|'|POS|_ file|file|NN|_ containing|contain|VBG|_ the|the|DT|_ transcript.gtf|transcript.gtf|JJ|_ output|output|NN|_ files|file|NNS|_ from|from|IN|_ culfflinks|culfflink|NNS|_ .|.|.|_ Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ merged.gtf|merged.gtf|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ cuffmerge|cuffmerge|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 00091313-Feb-2011|00091313-feb-2011|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ each|each|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ isolated|isolate|VBN|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_ .|.|.|_ The|the|DT|_ 30|30|CD|_ mL|ml|NN|_ culture|culture|NN|_ was|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ three|three|CD|_ 15|15|CD|_ mL|ml|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ EtOH/Phenol|etoh/phenol|NN|_ stop|stop|VB|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ pH|ph|NN|_ 4.2|4.2|CD|_ -LSB-|-lsb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RSB-|-rsb-|-RRB-|_ in|in|IN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 4,000|4,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ suspended|suspend|VBN|_ in|in|IN|_ 800|800|CD|_ µL|µl|NN|_ TE|TE|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ .|.|.|_ SDS|sds|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ µL|µl|NN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ samples|sample|NNS|_ mixed|mix|VBN|_ by|by|IN|_ inversion|inversion|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 88|88|CD|_ µL|µl|NN|_ 1|1|CD|_ M|m|NN|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ -LRB-|-lrb-|-LRB-|_ 1mL|1ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.2|4.2|CD|_ ,|,|,|_ 65|65|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 6|6|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ solution|solution|NN|_ was|be|VBD|_ separated|separate|VBN|_ into|into|IN|_ layers|layer|NNS|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ upper|upper|JJ|_ aqueous|aqueous|JJ|_ RNA|rna|NN|_ containing|contain|VBG|_ layer|layer|NN|_ removed|remove|VBD|_ and|and|CC|_ transferred|transfer|VBD|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ by|by|IN|_ three|three|CD|_ extractions|extraction|NNS|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ CHCl3|chcl3|NN|_ :|:|:|_ IAA|iaa|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ precipitated|precipitated|JJ|_ -LRB-|-lrb-|-LRB-|_ -80|-80|CD|_ °C|°c|NN|_ ,|,|,|_ O/N|o/n|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1/10|1/10|CD|_ volume|volume|NN|_ of|of|IN|_ 3M|3M|NNP|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2|2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice|ice|NN|_ cold|cold|JJ|_ 100|100|CD|_ %|%|NN|_ EtOH|etoh|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ supernatant|supernatant|JJ|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ 75|75|CD|_ %|%|NN|_ cold|cold|JJ|_ EtOH|etoh|NN|_ -LRB-|-lrb-|-LRB-|_ made|make|VBN|_ with|with|IN|_ DEPC-treated|depc-treated|JJ|_ water|water|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ air|air|NN|_ dried|dry|VBD|_ before|before|IN|_ suspension|suspension|NN|_ in|in|IN|_ 80|80|CD|_ µL|µl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ 10|10|CD|_ X|x|NN|_ Turbo|Turbo|NNP|_ DNAse|dnase|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ RNA|rna|NN|_ solution|solution|NN|_ .|.|.|_ 1|1|CD|_ µL|µl|NN|_ of|of|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ solution|solution|NN|_ ,|,|,|_ which|which|WDT|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ DNase|dnase|NN|_ Inactivation|inactivation|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ occasional|occasional|JJ|_ mixing|mix|VBG|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ microfuge|microfuge|NN|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ tested|test|VBN|_ using|use|VBG|_ the|the|DT|_ the|the|DT|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ analysed|analyse|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ each|each|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ isolated|isolate|VBN|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_ .|.|.|_ The|the|DT|_ 30|30|CD|_ mL|ml|NN|_ culture|culture|NN|_ was|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ three|three|CD|_ 15|15|CD|_ mL|ml|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ EtOH/Phenol|etoh/phenol|NN|_ stop|stop|VB|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ pH|ph|NN|_ 4.2|4.2|CD|_ -LSB-|-lsb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RSB-|-rsb-|-RRB-|_ in|in|IN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 4,000|4,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ suspended|suspend|VBN|_ in|in|IN|_ 800|800|CD|_ µL|µl|NN|_ TE|TE|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mg/mL|mg/ml|NN|_ lysozyme|lysozyme|NN|_ .|.|.|_ SDS|sds|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ µL|µl|NN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w/v|w/v|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ samples|sample|NNS|_ mixed|mix|VBN|_ by|by|IN|_ inversion|inversion|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 88|88|CD|_ µL|µl|NN|_ 1|1|CD|_ M|m|NN|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ -LRB-|-lrb-|-LRB-|_ 1mL|1ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.2|4.2|CD|_ ,|,|,|_ 65|65|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ 6|6|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ solution|solution|NN|_ was|be|VBD|_ separated|separate|VBN|_ into|into|IN|_ layers|layer|NNS|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ upper|upper|JJ|_ aqueous|aqueous|JJ|_ RNA|rna|NN|_ containing|contain|VBG|_ layer|layer|NN|_ removed|remove|VBD|_ and|and|CC|_ transferred|transfer|VBD|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ by|by|IN|_ three|three|CD|_ extractions|extraction|NNS|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ CHCl3|chcl3|NN|_ :|:|:|_ IAA|iaa|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ being|be|VBG|_ precipitated|precipitated|JJ|_ -LRB-|-lrb-|-LRB-|_ -80|-80|CD|_ °C|°c|NN|_ ,|,|,|_ O/N|o/n|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1/10|1/10|CD|_ volume|volume|NN|_ of|of|IN|_ 3M|3M|NNP|_ NaOAc|naoac|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.2|5.2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2|2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice|ice|NN|_ cold|cold|JJ|_ 100|100|CD|_ %|%|NN|_ EtOH|etoh|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ supernatant|supernatant|JJ|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ 75|75|CD|_ %|%|NN|_ cold|cold|JJ|_ EtOH|etoh|NN|_ -LRB-|-lrb-|-LRB-|_ made|make|VBN|_ with|with|IN|_ DEPC-treated|depc-treated|JJ|_ water|water|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ air|air|NN|_ dried|dry|VBD|_ before|before|IN|_ suspension|suspension|NN|_ in|in|IN|_ 80|80|CD|_ µL|µl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ 10|10|CD|_ X|x|NN|_ Turbo|Turbo|NNP|_ DNAse|dnase|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ RNA|rna|NN|_ solution|solution|NN|_ .|.|.|_ 1|1|CD|_ µL|µl|NN|_ of|of|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ solution|solution|NN|_ ,|,|,|_ which|which|WDT|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ DNase|dnase|NN|_ Inactivation|inactivation|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ occasional|occasional|JJ|_ mixing|mix|VBG|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ microfuge|microfuge|NN|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ tested|test|VBN|_ using|use|VBG|_ the|the|DT|_ the|the|DT|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ analysed|analyse|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
200|200|CD|_ bp|bp|NN|_ insert|insert|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depletion|depletion|NN|_
Synchronization|synchronization|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ passaging|passaging|NN|_ cells|cell|NNS|_ through|through|IN|_ one|one|CD|_ or|or|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase according|accord|VBG|_ to|to|TO|_ Cutler|Cutler|NNP|_ and|and|CC|_ Evans|Evans|NNP|_ 1966|1966|CD|_ .|.|.|_ Briefly|briefly|RB|_ :|:|:|_ Individual|individual|JJ|_ colonies|colony|NNS|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ plate|plate|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 24|24|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ O/N|o/n|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|_ media|media|NNS|_ was|be|VBD|_ inoculated|inoculate|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ early-logarithmic|early-logarithmic|JJ|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ maintained|maintain|VBN|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ approximately|approximately|RB|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ An|a|DT|_ appropriate|appropriate|JJ|_ amount|amount|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ pre-warmed|pre-warmed|JJ|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ media|media|NNS|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ approximate|approximate|JJ|_ 7-fold|7-fold|JJ|_ dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Released|release|VBN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ harvested|harvest|VBN|_ -LRB-|-lrb-|-LRB-|_ time|time|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ or|or|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ GCC|gcc|NN|_ and|and|CC|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ also|also|RB|_ taken|take|VBN|_ for|for|IN|_ FACS|facs|NN|_ analysis|analysis|NN|_ and|and|CC|_ fluorescence|fluorescence|NN|_ microscopy|microscopy|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Stationary|stationary|JJ|_ phase|phase|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ sampled|sample|VBN|_ at|at|IN|_ times|time|NNS|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hour|hour|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hours|hour|NNS|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_
RNA-Seq|rna-seq|NN|_
time|time|NN|_ post|post|NN|_ release|release|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ immediately|immediately|RB|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ Stationary|stationary|JJ|_ phase|phase|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ replicate|replicate|VBP|_ 2|2|CD|_
Synchronization|synchronization|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ passaging|passaging|NN|_ cells|cell|NNS|_ through|through|IN|_ one|one|CD|_ or|or|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase according|accord|VBG|_ to|to|TO|_ Cutler|Cutler|NNP|_ and|and|CC|_ Evans|Evans|NNP|_ 1966|1966|CD|_ .|.|.|_ Briefly|briefly|RB|_ :|:|:|_ Individual|individual|JJ|_ colonies|colony|NNS|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ plate|plate|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 24|24|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ O/N|o/n|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ M9|m9|NN|_ media|media|NNS|_ was|be|VBD|_ inoculated|inoculate|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ early-logarithmic|early-logarithmic|JJ|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ maintained|maintain|VBN|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ approximately|approximately|RB|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ An|a|DT|_ appropriate|appropriate|JJ|_ amount|amount|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ pre-warmed|pre-warmed|JJ|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ media|media|NNS|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -LRB-|-lrb-|-LRB-|_ approximate|approximate|JJ|_ 7-fold|7-fold|JJ|_ dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Released|release|VBN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ harvested|harvest|VBN|_ -LRB-|-lrb-|-LRB-|_ time|time|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ or|or|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ GCC|gcc|NN|_ and|and|CC|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_ Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ also|also|RB|_ taken|take|VBN|_ for|for|IN|_ FACS|facs|NN|_ analysis|analysis|NN|_ and|and|CC|_ fluorescence|fluorescence|NN|_ microscopy|microscopy|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hr|hr|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Stationary|stationary|JJ|_ phase|phase|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ sampled|sample|VBN|_ at|at|IN|_ times|time|NNS|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hour|hour|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hours|hour|NNS|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_
Justin|Justin|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ O|o|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Sullivan|Sullivan|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ performed|perform|VBN|_ with|with|IN|_ RTA|rta|NN|_ v1|v1|NN|_ .18.5|.18.5|CD|_
the|the|DT|_ first|first|JJ|_ ten|ten|CD|_ base|base|NN|_ pairs|pair|NNS|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ FASTXToolkit|fastxtoolkit|NN|_ 0.0.13|0.0.13|CD|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ mapped|map|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.5|0.7.5|CD|_ a|a|DT|_
The|the|DT|_ number|number|NN|_ read|read|VBD|_ pairs|pair|NNS|_ mapped|map|VBN|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ with|with|IN|_ HTSeq|htseq|NN|_ 0.6.1|0.6.1|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ A|a|DT|_ tab|tab|NN|_ deliminited|deliminit|VBN|_ file|file|NN|_ with|with|IN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ 200|200|CD|_ µL|µl|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ by|by|IN|_ pelleting|pelleting|NN|_ and|and|CC|_ resuspeding|resuspeding|NN|_ in|in|IN|_ 500|500|CD|_ µL|µl|NN|_ of|of|IN|_ Trizol|trizol|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ purification|purification|NN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ Direct-Zol|Direct-Zol|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ received|receive|VBD|_ two|two|CD|_ 30-minute|30-minute|JJ|_ DNase|dnase|NN|_ treatments|treatment|NNS|_ using|use|VBG|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Three|three|CD|_ samples|sample|NNS|_ were|be|VBD|_ prepped|prep|VBN|_ from|from|IN|_ each|each|DT|_ culture|culture|NN|_ and|and|CC|_ pooled|pool|VBD|_ to|to|TO|_ generate|generate|VB|_ sufficient|sufficient|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW27786|bw27786|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ derivative|derivative|NN|_ -RRB-|-rrb-|-RRB-|_
rpos|rpo|NNS|_ level|level|NN|_ :|:|:|_ 100|100|CD|_ %|%|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
Daniel|Daniel|NNP|_ ,|,|,|_ ,|,|,|_ Stoebel|Stoebel|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ performed|perform|VBN|_ with|with|IN|_ RTA|rta|NN|_ v1|v1|NN|_ .18.5|.18.5|CD|_
the|the|DT|_ first|first|JJ|_ ten|ten|CD|_ base|base|NN|_ pairs|pair|NNS|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ FASTXToolkit|fastxtoolkit|NN|_ 0.0.13|0.0.13|CD|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ mapped|map|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.5|0.7.5|CD|_ a|a|DT|_
The|the|DT|_ number|number|NN|_ read|read|VBD|_ pairs|pair|NNS|_ mapped|map|VBN|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ with|with|IN|_ HTSeq|htseq|NN|_ 0.6.1|0.6.1|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ A|a|DT|_ tab|tab|NN|_ deliminited|deliminit|VBN|_ file|file|NN|_ with|with|IN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ 200|200|CD|_ µL|µl|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ by|by|IN|_ pelleting|pelleting|NN|_ and|and|CC|_ resuspeding|resuspeding|NN|_ in|in|IN|_ 500|500|CD|_ µL|µl|NN|_ of|of|IN|_ Trizol|trizol|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ purification|purification|NN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ Direct-Zol|Direct-Zol|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ received|receive|VBD|_ two|two|CD|_ 30-minute|30-minute|JJ|_ DNase|dnase|NN|_ treatments|treatment|NNS|_ using|use|VBG|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Three|three|CD|_ samples|sample|NNS|_ were|be|VBD|_ prepped|prep|VBN|_ from|from|IN|_ each|each|DT|_ culture|culture|NN|_ and|and|CC|_ pooled|pool|VBD|_ to|to|TO|_ generate|generate|VB|_ sufficient|sufficient|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DMS2545|dms2545|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ derivative|derivative|NN|_ -RRB-|-rrb-|-RRB-|_
rpos|rpo|NNS|_ level|level|NN|_ :|:|:|_ 0|0|CD|_ %|%|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
Daniel|Daniel|NNP|_ ,|,|,|_ ,|,|,|_ Stoebel|Stoebel|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ performed|perform|VBN|_ with|with|IN|_ RTA|rta|NN|_ v1|v1|NN|_ .18.5|.18.5|CD|_
the|the|DT|_ first|first|JJ|_ ten|ten|CD|_ base|base|NN|_ pairs|pair|NNS|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ FASTXToolkit|fastxtoolkit|NN|_ 0.0.13|0.0.13|CD|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ mapped|map|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.5|0.7.5|CD|_ a|a|DT|_
The|the|DT|_ number|number|NN|_ read|read|VBD|_ pairs|pair|NNS|_ mapped|map|VBN|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ with|with|IN|_ HTSeq|htseq|NN|_ 0.6.1|0.6.1|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ A|a|DT|_ tab|tab|NN|_ deliminited|deliminit|VBN|_ file|file|NN|_ with|with|IN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ 200|200|CD|_ µL|µl|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ by|by|IN|_ pelleting|pelleting|NN|_ and|and|CC|_ resuspeding|resuspeding|NN|_ in|in|IN|_ 500|500|CD|_ µL|µl|NN|_ of|of|IN|_ Trizol|trizol|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ purification|purification|NN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ Direct-Zol|Direct-Zol|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ received|receive|VBD|_ two|two|CD|_ 30-minute|30-minute|JJ|_ DNase|dnase|NN|_ treatments|treatment|NNS|_ using|use|VBG|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Three|three|CD|_ samples|sample|NNS|_ were|be|VBD|_ prepped|prep|VBN|_ from|from|IN|_ each|each|DT|_ culture|culture|NN|_ and|and|CC|_ pooled|pool|VBD|_ to|to|TO|_ generate|generate|VB|_ sufficient|sufficient|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DMS2564|dms2564|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ derivative|derivative|NN|_ -RRB-|-rrb-|-RRB-|_
rpos|rpo|NNS|_ level|level|NN|_ :|:|:|_ 26|26|CD|_ %|%|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
Daniel|Daniel|NNP|_ ,|,|,|_ ,|,|,|_ Stoebel|Stoebel|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ performed|perform|VBN|_ with|with|IN|_ RTA|rta|NN|_ v1|v1|NN|_ .18.5|.18.5|CD|_
the|the|DT|_ first|first|JJ|_ ten|ten|CD|_ base|base|NN|_ pairs|pair|NNS|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ FASTXToolkit|fastxtoolkit|NN|_ 0.0.13|0.0.13|CD|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ mapped|map|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.5|0.7.5|CD|_ a|a|DT|_
The|the|DT|_ number|number|NN|_ read|read|VBD|_ pairs|pair|NNS|_ mapped|map|VBN|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ with|with|IN|_ HTSeq|htseq|NN|_ 0.6.1|0.6.1|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ A|a|DT|_ tab|tab|NN|_ deliminited|deliminit|VBN|_ file|file|NN|_ with|with|IN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ 200|200|CD|_ µL|µl|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ by|by|IN|_ pelleting|pelleting|NN|_ and|and|CC|_ resuspeding|resuspeding|NN|_ in|in|IN|_ 500|500|CD|_ µL|µl|NN|_ of|of|IN|_ Trizol|trizol|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ purification|purification|NN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ Direct-Zol|Direct-Zol|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ received|receive|VBD|_ two|two|CD|_ 30-minute|30-minute|JJ|_ DNase|dnase|NN|_ treatments|treatment|NNS|_ using|use|VBG|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Three|three|CD|_ samples|sample|NNS|_ were|be|VBD|_ prepped|prep|VBN|_ from|from|IN|_ each|each|DT|_ culture|culture|NN|_ and|and|CC|_ pooled|pool|VBD|_ to|to|TO|_ generate|generate|VB|_ sufficient|sufficient|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW27786|bw27786|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ derivative|derivative|NN|_ -RRB-|-rrb-|-RRB-|_
rpos|rpo|NNS|_ level|level|NN|_ :|:|:|_ 100|100|CD|_ %|%|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
Daniel|Daniel|NNP|_ ,|,|,|_ ,|,|,|_ Stoebel|Stoebel|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ performed|perform|VBN|_ with|with|IN|_ RTA|rta|NN|_ v1|v1|NN|_ .18.5|.18.5|CD|_
the|the|DT|_ first|first|JJ|_ ten|ten|CD|_ base|base|NN|_ pairs|pair|NNS|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ FASTXToolkit|fastxtoolkit|NN|_ 0.0.13|0.0.13|CD|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ mapped|map|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.5|0.7.5|CD|_ a|a|DT|_
The|the|DT|_ number|number|NN|_ read|read|VBD|_ pairs|pair|NNS|_ mapped|map|VBN|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ with|with|IN|_ HTSeq|htseq|NN|_ 0.6.1|0.6.1|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ A|a|DT|_ tab|tab|NN|_ deliminited|deliminit|VBN|_ file|file|NN|_ with|with|IN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ 200|200|CD|_ µL|µl|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ by|by|IN|_ pelleting|pelleting|NN|_ and|and|CC|_ resuspeding|resuspeding|NN|_ in|in|IN|_ 500|500|CD|_ µL|µl|NN|_ of|of|IN|_ Trizol|trizol|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ purification|purification|NN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ Direct-Zol|Direct-Zol|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ received|receive|VBD|_ two|two|CD|_ 30-minute|30-minute|JJ|_ DNase|dnase|NN|_ treatments|treatment|NNS|_ using|use|VBG|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Three|three|CD|_ samples|sample|NNS|_ were|be|VBD|_ prepped|prep|VBN|_ from|from|IN|_ each|each|DT|_ culture|culture|NN|_ and|and|CC|_ pooled|pool|VBD|_ to|to|TO|_ generate|generate|VB|_ sufficient|sufficient|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DMS2545|dms2545|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ derivative|derivative|NN|_ -RRB-|-rrb-|-RRB-|_
rpos|rpo|NNS|_ level|level|NN|_ :|:|:|_ 0|0|CD|_ %|%|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
Daniel|Daniel|NNP|_ ,|,|,|_ ,|,|,|_ Stoebel|Stoebel|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ performed|perform|VBN|_ with|with|IN|_ RTA|rta|NN|_ v1|v1|NN|_ .18.5|.18.5|CD|_
the|the|DT|_ first|first|JJ|_ ten|ten|CD|_ base|base|NN|_ pairs|pair|NNS|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ FASTXToolkit|fastxtoolkit|NN|_ 0.0.13|0.0.13|CD|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ mapped|map|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.5|0.7.5|CD|_ a|a|DT|_
The|the|DT|_ number|number|NN|_ read|read|VBD|_ pairs|pair|NNS|_ mapped|map|VBN|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ with|with|IN|_ HTSeq|htseq|NN|_ 0.6.1|0.6.1|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ A|a|DT|_ tab|tab|NN|_ deliminited|deliminit|VBN|_ file|file|NN|_ with|with|IN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ 200|200|CD|_ µL|µl|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ by|by|IN|_ pelleting|pelleting|NN|_ and|and|CC|_ resuspeding|resuspeding|NN|_ in|in|IN|_ 500|500|CD|_ µL|µl|NN|_ of|of|IN|_ Trizol|trizol|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ purification|purification|NN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ Direct-Zol|Direct-Zol|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ received|receive|VBD|_ two|two|CD|_ 30-minute|30-minute|JJ|_ DNase|dnase|NN|_ treatments|treatment|NNS|_ using|use|VBG|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Three|three|CD|_ samples|sample|NNS|_ were|be|VBD|_ prepped|prep|VBN|_ from|from|IN|_ each|each|DT|_ culture|culture|NN|_ and|and|CC|_ pooled|pool|VBD|_ to|to|TO|_ generate|generate|VB|_ sufficient|sufficient|JJ|_ RNA|rna|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DMS2564|dms2564|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ derivative|derivative|NN|_ -RRB-|-rrb-|-RRB-|_
rpos|rpo|NNS|_ level|level|NN|_ :|:|:|_ 26|26|CD|_ %|%|NN|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_
Daniel|Daniel|NNP|_ ,|,|,|_ ,|,|,|_ Stoebel|Stoebel|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ deltaprfC|deltaprfc|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ deltaprfC|deltaprfc|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ prfB-Bstrain|prfb-bstrain|JJ|_ allele|allele|NN|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ prfB-Bstrain|prfb-bstrain|JJ|_ allele|allele|NN|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ prfB-Bstrain|prfb-bstrain|JJ|_ allele|allele|NN|_ deltaprfC|deltaprfc|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ prfB-Bstrain|prfb-bstrain|JJ|_ allele|allele|NN|_ deltaprfC|deltaprfc|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ prfB-Bstrain|prfb-bstrain|JJ|_ allele|allele|NN|_ deltaprfC|deltaprfc|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ prfB-Bstrain|prfb-bstrain|JJ|_ allele|allele|NN|_ deltaprfC|deltaprfc|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ prfB-Bstrain|prfb-bstrain|JJ|_ allele|allele|NN|_ deltaprfC|deltaprfc|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBD|_ and|and|CC|_ indexed|index|VBD|_ using|use|VBG|_ SAMtools|SAMtools|NNP|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ deltaprfC|deltaprfc|NN|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Natalie|Natalie|NNP|_ ,|,|,|_ ,|,|,|_ Baggett|Baggett|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ For|for|IN|_ culture|culture|NN|_ tube|tube|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ and|and|CC|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ ΔompR|δompr|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ of|of|IN|_ NaCl|nacl|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ ΔompR|δompr|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ of|of|IN|_ NaCl|nacl|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ ΔompR|δompr|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ of|of|IN|_ NaCl|nacl|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ ΔompR|δompr|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ of|of|IN|_ NaCl|nacl|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ ΔompR|δompr|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ of|of|IN|_ NaCl|nacl|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ ompR|ompr|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ ΔompR|δompr|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ of|of|IN|_ NaCl|nacl|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ ΔompR|δompr|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ of|of|IN|_ NaCl|nacl|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ ompR|ompr|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ ΔompR|δompr|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ of|of|IN|_ NaCl|nacl|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Donghyuk|donghyuk|NN|_ ,|,|,|_ ,|,|,|_ Kim|Kim|NNP|_
All|All|NNP|_ data|datum|NNS|_ was|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ Ver|Ver|NNP|_ .2.03|.2.03|CD|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ an|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ automatic|automatic|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ bacterial|bacterial|JJ|_ RNA-seq|rna-seq|NN|_ analysis|analysis|NN|_ tool|tool|NN|_ ;|;|:|_ for|for|IN|_ additional|additional|JJ|_ information|information|NN|_ see|see|VB|_ :|:|:|_ McClure|McClure|NNP|_ ,|,|,|_ R.|R.|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Computational|computational|JJ|_ analysis|analysis|NN|_ of|of|IN|_ bacterial|bacterial|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Nucleic|nucleic|JJ|_ Acids|acid|NNS|_ Res|Res|NNP|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e140|e140|NN|_ .|.|.|_ The|the|DT|_ default|default|NN|_ general|general|JJ|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ with|with|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ verbose|verbose|JJ|_ output|output|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tab|tab|NN|_ ticked|tick|VBD|_ and|and|CC|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ orientation|orientation|NN|_ of|of|IN|_ mate-pair|mate-pair|JJ|_ reads|read|VBZ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ changed|change|VBD|_ to|to|TO|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ rf|rf|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 017644.1|017644.1|CD|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism NA114|na114|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ txt|txt|NN|_ ,|,|,|_ *|*|SYM|_ xml|xml|NN|_ :|:|:|_ These|these|DT|_ files|file|NNS|_ contain|contain|VBP|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ ,|,|,|_ normalized|normalize|VBD|_ counts|count|NNS|_ ,|,|,|_ RPKM|rpkm|NN|_ values|value|NNS|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ ,|,|,|_ P-values|p-value|NNS|_ and|and|CC|_ Q-values|q-value|NNS|_ .|.|.|_ Each|each|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ values|value|NNS|_ for|for|IN|_ both|both|DT|_ samples|sample|NNS|_ at|at|IN|_ the|the|DT|_ indicated|indicate|VBN|_ timepoint|timepoint|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ a|a|DT|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ GeneJET|GeneJET|NNP|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ .|.|.|_
Extraction|extraction|NN|_ followed|follow|VBN|_ by|by|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ from|from|IN|_ Ambion|Ambion|NNP|_ .|.|.|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ Ribo-zero|ribo-zero|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Followed|follow|VBN|_ by|by|IN|_ RNA-seq|rna-seq|JJ|_ library|library|NN|_ prep|prep|NN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
isolate|isolate|NN|_ :|:|:|_ UR40|ur40|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
Rasmus|Rasmus|NNP|_ ,|,|,|_ Nielsen|Nielsen|NNP|_ ,|,|,|_ Klitgaard|Klitgaard|NNP|_
All|All|NNP|_ data|datum|NNS|_ was|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ Ver|Ver|NNP|_ .2.03|.2.03|CD|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ an|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ automatic|automatic|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ bacterial|bacterial|JJ|_ RNA-seq|rna-seq|NN|_ analysis|analysis|NN|_ tool|tool|NN|_ ;|;|:|_ for|for|IN|_ additional|additional|JJ|_ information|information|NN|_ see|see|VB|_ :|:|:|_ McClure|McClure|NNP|_ ,|,|,|_ R.|R.|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Computational|computational|JJ|_ analysis|analysis|NN|_ of|of|IN|_ bacterial|bacterial|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Nucleic|nucleic|JJ|_ Acids|acid|NNS|_ Res|Res|NNP|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e140|e140|NN|_ .|.|.|_ The|the|DT|_ default|default|NN|_ general|general|JJ|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ with|with|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ verbose|verbose|JJ|_ output|output|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tab|tab|NN|_ ticked|tick|VBD|_ and|and|CC|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ orientation|orientation|NN|_ of|of|IN|_ mate-pair|mate-pair|JJ|_ reads|read|VBZ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ changed|change|VBD|_ to|to|TO|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ rf|rf|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 017644.1|017644.1|CD|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism NA114|na114|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ txt|txt|NN|_ ,|,|,|_ *|*|SYM|_ xml|xml|NN|_ :|:|:|_ These|these|DT|_ files|file|NNS|_ contain|contain|VBP|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ ,|,|,|_ normalized|normalize|VBD|_ counts|count|NNS|_ ,|,|,|_ RPKM|rpkm|NN|_ values|value|NNS|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ ,|,|,|_ P-values|p-value|NNS|_ and|and|CC|_ Q-values|q-value|NNS|_ .|.|.|_ Each|each|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ values|value|NNS|_ for|for|IN|_ both|both|DT|_ samples|sample|NNS|_ at|at|IN|_ the|the|DT|_ indicated|indicate|VBN|_ timepoint|timepoint|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ a|a|DT|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ GeneJET|GeneJET|NNP|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ .|.|.|_
Extraction|extraction|NN|_ followed|follow|VBN|_ by|by|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ from|from|IN|_ Ambion|Ambion|NNP|_ .|.|.|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ Ribo-zero|ribo-zero|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Followed|follow|VBN|_ by|by|IN|_ RNA-seq|rna-seq|JJ|_ library|library|NN|_ prep|prep|NN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
isolate|isolate|NN|_ :|:|:|_ UR40|ur40|NN|_
treatment|treatment|NN|_ :|:|:|_ ciprofloxacin|ciprofloxacin|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
Rasmus|Rasmus|NNP|_ ,|,|,|_ Nielsen|Nielsen|NNP|_ ,|,|,|_ Klitgaard|Klitgaard|NNP|_
All|All|NNP|_ data|datum|NNS|_ was|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ Ver|Ver|NNP|_ .2.03|.2.03|CD|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ an|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ automatic|automatic|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ bacterial|bacterial|JJ|_ RNA-seq|rna-seq|NN|_ analysis|analysis|NN|_ tool|tool|NN|_ ;|;|:|_ for|for|IN|_ additional|additional|JJ|_ information|information|NN|_ see|see|VB|_ :|:|:|_ McClure|McClure|NNP|_ ,|,|,|_ R.|R.|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Computational|computational|JJ|_ analysis|analysis|NN|_ of|of|IN|_ bacterial|bacterial|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Nucleic|nucleic|JJ|_ Acids|acid|NNS|_ Res|Res|NNP|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e140|e140|NN|_ .|.|.|_ The|the|DT|_ default|default|NN|_ general|general|JJ|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ with|with|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ verbose|verbose|JJ|_ output|output|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tab|tab|NN|_ ticked|tick|VBD|_ and|and|CC|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ orientation|orientation|NN|_ of|of|IN|_ mate-pair|mate-pair|JJ|_ reads|read|VBZ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ changed|change|VBD|_ to|to|TO|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ rf|rf|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 017644.1|017644.1|CD|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism NA114|na114|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ txt|txt|NN|_ ,|,|,|_ *|*|SYM|_ xml|xml|NN|_ :|:|:|_ These|these|DT|_ files|file|NNS|_ contain|contain|VBP|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ ,|,|,|_ normalized|normalize|VBD|_ counts|count|NNS|_ ,|,|,|_ RPKM|rpkm|NN|_ values|value|NNS|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ ,|,|,|_ P-values|p-value|NNS|_ and|and|CC|_ Q-values|q-value|NNS|_ .|.|.|_ Each|each|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ values|value|NNS|_ for|for|IN|_ both|both|DT|_ samples|sample|NNS|_ at|at|IN|_ the|the|DT|_ indicated|indicate|VBN|_ timepoint|timepoint|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ a|a|DT|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ GeneJET|GeneJET|NNP|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ .|.|.|_
Extraction|extraction|NN|_ followed|follow|VBN|_ by|by|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ from|from|IN|_ Ambion|Ambion|NNP|_ .|.|.|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ Ribo-zero|ribo-zero|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Followed|follow|VBN|_ by|by|IN|_ RNA-seq|rna-seq|JJ|_ library|library|NN|_ prep|prep|NN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
isolate|isolate|NN|_ :|:|:|_ UR40|ur40|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
Rasmus|Rasmus|NNP|_ ,|,|,|_ Nielsen|Nielsen|NNP|_ ,|,|,|_ Klitgaard|Klitgaard|NNP|_
All|All|NNP|_ data|datum|NNS|_ was|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ Ver|Ver|NNP|_ .2.03|.2.03|CD|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ an|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ automatic|automatic|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ bacterial|bacterial|JJ|_ RNA-seq|rna-seq|NN|_ analysis|analysis|NN|_ tool|tool|NN|_ ;|;|:|_ for|for|IN|_ additional|additional|JJ|_ information|information|NN|_ see|see|VB|_ :|:|:|_ McClure|McClure|NNP|_ ,|,|,|_ R.|R.|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Computational|computational|JJ|_ analysis|analysis|NN|_ of|of|IN|_ bacterial|bacterial|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Nucleic|nucleic|JJ|_ Acids|acid|NNS|_ Res|Res|NNP|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e140|e140|NN|_ .|.|.|_ The|the|DT|_ default|default|NN|_ general|general|JJ|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ with|with|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ verbose|verbose|JJ|_ output|output|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tab|tab|NN|_ ticked|tick|VBD|_ and|and|CC|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ orientation|orientation|NN|_ of|of|IN|_ mate-pair|mate-pair|JJ|_ reads|read|VBZ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ changed|change|VBD|_ to|to|TO|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ rf|rf|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 017644.1|017644.1|CD|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism NA114|na114|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ txt|txt|NN|_ ,|,|,|_ *|*|SYM|_ xml|xml|NN|_ :|:|:|_ These|these|DT|_ files|file|NNS|_ contain|contain|VBP|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ ,|,|,|_ normalized|normalize|VBD|_ counts|count|NNS|_ ,|,|,|_ RPKM|rpkm|NN|_ values|value|NNS|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ ,|,|,|_ P-values|p-value|NNS|_ and|and|CC|_ Q-values|q-value|NNS|_ .|.|.|_ Each|each|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ values|value|NNS|_ for|for|IN|_ both|both|DT|_ samples|sample|NNS|_ at|at|IN|_ the|the|DT|_ indicated|indicate|VBN|_ timepoint|timepoint|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ a|a|DT|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ GeneJET|GeneJET|NNP|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ .|.|.|_
Extraction|extraction|NN|_ followed|follow|VBN|_ by|by|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ from|from|IN|_ Ambion|Ambion|NNP|_ .|.|.|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ Ribo-zero|ribo-zero|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Followed|follow|VBN|_ by|by|IN|_ RNA-seq|rna-seq|JJ|_ library|library|NN|_ prep|prep|NN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
isolate|isolate|NN|_ :|:|:|_ UR40|ur40|NN|_
treatment|treatment|NN|_ :|:|:|_ ciprofloxacin|ciprofloxacin|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
Rasmus|Rasmus|NNP|_ ,|,|,|_ Nielsen|Nielsen|NNP|_ ,|,|,|_ Klitgaard|Klitgaard|NNP|_
All|All|NNP|_ data|datum|NNS|_ was|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ Ver|Ver|NNP|_ .2.03|.2.03|CD|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ an|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ automatic|automatic|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ bacterial|bacterial|JJ|_ RNA-seq|rna-seq|NN|_ analysis|analysis|NN|_ tool|tool|NN|_ ;|;|:|_ for|for|IN|_ additional|additional|JJ|_ information|information|NN|_ see|see|VB|_ :|:|:|_ McClure|McClure|NNP|_ ,|,|,|_ R.|R.|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Computational|computational|JJ|_ analysis|analysis|NN|_ of|of|IN|_ bacterial|bacterial|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Nucleic|nucleic|JJ|_ Acids|acid|NNS|_ Res|Res|NNP|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e140|e140|NN|_ .|.|.|_ The|the|DT|_ default|default|NN|_ general|general|JJ|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ with|with|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ verbose|verbose|JJ|_ output|output|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tab|tab|NN|_ ticked|tick|VBD|_ and|and|CC|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ orientation|orientation|NN|_ of|of|IN|_ mate-pair|mate-pair|JJ|_ reads|read|VBZ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ changed|change|VBD|_ to|to|TO|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ rf|rf|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 017644.1|017644.1|CD|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism NA114|na114|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ txt|txt|NN|_ ,|,|,|_ *|*|SYM|_ xml|xml|NN|_ :|:|:|_ These|these|DT|_ files|file|NNS|_ contain|contain|VBP|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ ,|,|,|_ normalized|normalize|VBD|_ counts|count|NNS|_ ,|,|,|_ RPKM|rpkm|NN|_ values|value|NNS|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ ,|,|,|_ P-values|p-value|NNS|_ and|and|CC|_ Q-values|q-value|NNS|_ .|.|.|_ Each|each|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ values|value|NNS|_ for|for|IN|_ both|both|DT|_ samples|sample|NNS|_ at|at|IN|_ the|the|DT|_ indicated|indicate|VBN|_ timepoint|timepoint|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ a|a|DT|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ GeneJET|GeneJET|NNP|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ .|.|.|_
Extraction|extraction|NN|_ followed|follow|VBN|_ by|by|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ from|from|IN|_ Ambion|Ambion|NNP|_ .|.|.|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ Ribo-zero|ribo-zero|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Followed|follow|VBN|_ by|by|IN|_ RNA-seq|rna-seq|JJ|_ library|library|NN|_ prep|prep|NN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
isolate|isolate|NN|_ :|:|:|_ UR40|ur40|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 90|90|CD|_ min|min|NN|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
Rasmus|Rasmus|NNP|_ ,|,|,|_ Nielsen|Nielsen|NNP|_ ,|,|,|_ Klitgaard|Klitgaard|NNP|_
All|All|NNP|_ data|datum|NNS|_ was|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ Ver|Ver|NNP|_ .2.03|.2.03|CD|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ an|a|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ automatic|automatic|JJ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ bacterial|bacterial|JJ|_ RNA-seq|rna-seq|NN|_ analysis|analysis|NN|_ tool|tool|NN|_ ;|;|:|_ for|for|IN|_ additional|additional|JJ|_ information|information|NN|_ see|see|VB|_ :|:|:|_ McClure|McClure|NNP|_ ,|,|,|_ R.|R.|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Computational|computational|JJ|_ analysis|analysis|NN|_ of|of|IN|_ bacterial|bacterial|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ Nucleic|nucleic|JJ|_ Acids|acid|NNS|_ Res|Res|NNP|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e140|e140|NN|_ .|.|.|_ The|the|DT|_ default|default|NN|_ general|general|JJ|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ with|with|IN|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ verbose|verbose|JJ|_ output|output|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ tab|tab|NN|_ ticked|tick|VBD|_ and|and|CC|_ the|the|DT|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ orientation|orientation|NN|_ of|of|IN|_ mate-pair|mate-pair|JJ|_ reads|read|VBZ|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ changed|change|VBD|_ to|to|TO|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ rf|rf|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 017644.1|017644.1|CD|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism NA114|na114|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ txt|txt|NN|_ ,|,|,|_ *|*|SYM|_ xml|xml|NN|_ :|:|:|_ These|these|DT|_ files|file|NNS|_ contain|contain|VBP|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ ,|,|,|_ normalized|normalize|VBD|_ counts|count|NNS|_ ,|,|,|_ RPKM|rpkm|NN|_ values|value|NNS|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ ,|,|,|_ P-values|p-value|NNS|_ and|and|CC|_ Q-values|q-value|NNS|_ .|.|.|_ Each|each|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ values|value|NNS|_ for|for|IN|_ both|both|DT|_ samples|sample|NNS|_ at|at|IN|_ the|the|DT|_ indicated|indicate|VBN|_ timepoint|timepoint|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ a|a|DT|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ GeneJET|GeneJET|NNP|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ .|.|.|_
Extraction|extraction|NN|_ followed|follow|VBN|_ by|by|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ from|from|IN|_ Ambion|Ambion|NNP|_ .|.|.|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ Ribo-zero|ribo-zero|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Followed|follow|VBN|_ by|by|IN|_ RNA-seq|rna-seq|JJ|_ library|library|NN|_ prep|prep|NN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
isolate|isolate|NN|_ :|:|:|_ UR40|ur40|NN|_
treatment|treatment|NN|_ :|:|:|_ ciprofloxacin|ciprofloxacin|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 90|90|CD|_ min|min|NN|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg/mL|2µg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ time|time|NN|_ points|point|NNS|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
Rasmus|Rasmus|NNP|_ ,|,|,|_ Nielsen|Nielsen|NNP|_ ,|,|,|_ Klitgaard|Klitgaard|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBAD|pbad|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ None|none|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBADsigma32wt|pbadsigma32wt|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ None|none|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBAD|pbad|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ None|none|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBADsigma32wt|pbadsigma32wt|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ None|none|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBAD|pbad|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ None|none|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBADsigma32wt|pbadsigma32wt|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ None|none|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 42C|42c|NN|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 42C|42c|NN|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 42C|42c|NN|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 42C|42c|NN|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 42C|42c|NN|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 42C|42c|NN|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBAD|pbad|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ None|none|NN|_
replicate|replicate|VB|_ :|:|:|_ 4|4|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBADsigma32I54N|pbadsigma32i54n|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ None|none|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBADsigma32I54N|pbadsigma32i54n|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
induction|induction|NN|_ :|:|:|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ None|none|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Evan|Evan|NNP|_ ,|,|,|_ Thomas|Thomas|NNP|_ ,|,|,|_ Powers|Powers|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 25|25|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 45|45|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 75|75|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 210|210|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 330|330|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 25h|25h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 26h|26h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 28h|28h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 0-16h|0-16h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 0-15h|0-15h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 0-2h|0-2h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 25|25|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P3|p3|NN|_
time|time|NN|_ :|:|:|_ 25|25|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P1|p1|NN|_
time|time|NN|_ :|:|:|_ 25|25|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 45|45|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P3|p3|NN|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P1|p1|NN|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 210|210|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 25h|25h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P3|p3|NN|_
time|time|NN|_ :|:|:|_ 28h|28h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 28h|28h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P1|p1|NN|_
time|time|NN|_ :|:|:|_ 28h|28h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 25|25|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 45|45|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 75|75|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 210|210|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 330|330|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 25h|25h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 26h|26h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 28h|28h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 0-16h|0-16h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 0-15h|0-15h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
time|time|NN|_ :|:|:|_ 0-2h|0-2h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 25|25|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P3|p3|NN|_
time|time|NN|_ :|:|:|_ 25|25|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P1|p1|NN|_
time|time|NN|_ :|:|:|_ 25|25|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 45|45|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 75|75|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P3|p3|NN|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P1|p1|NN|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 210|210|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 330|330|CD|_ min|min|NN|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 25h|25h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 26h|26h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
time|time|NN|_ :|:|:|_ 28h|28h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P3|p3|NN|_
time|time|NN|_ :|:|:|_ 28h|28h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
The|The|NNP|_ bcl2fastq|bcl2fastq|NNP|_ Conversion|Conversion|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ translate|translate|VB|_ cluster|cluster|NN|_ intensity|intensity|NN|_ values|value|NNS|_ into|into|IN|_ fastq|fastq|NN|_ files|file|NNS|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|IN|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http://genome.ucsc.edu|http://genome.ucsc.edu|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ chosen|choose|VBN|_ reference|reference|NN|_ sequence|sequence|NN|_ applying|apply|VBG|_ HTseq-count|htseq-count|JJ|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ in|in|IN|_ the|the|DT|_ intersection-nonempty|intersection-nonempty|JJ|_ mode|mode|NN|_ .|.|.|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P1|p1|NN|_
time|time|NN|_ :|:|:|_ 28h|28h|JJ|_
replicate|replicate|VBP|_ :|:|:|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Joana|Joana|NNP|_ ,|,|,|_ Danica|Danica|NNP|_ ,|,|,|_ Simen|Simen|NNP|_
For|for|IN|_ the|the|DT|_ whole-transcriptome|whole-transcriptome|JJ|_ analysis|analysis|NN|_ ,|,|,|_ sequencing|sequencing|NN|_ was|be|VBD|_ verified|verify|VBN|_ using|use|VBG|_ FASTQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.11.2|0.11.2|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ confirm|confirm|VB|_ base-call|base-call|JJ|_ quality|quality|NN|_ in|in|IN|_ each|each|DT|_ indexed|index|VBN|_ file|file|NN|_ .|.|.|_
Indices|Indices|NNPS|_ corresponding|correspond|VBG|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ were|be|VBD|_ merged|merge|VBN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ uploaded|upload|VBD|_ to|to|TO|_ a|a|DT|_ cloud-based|cloud-based|JJ|_ variant|variant|NN|_ of|of|IN|_ Galaxy|Galaxy|NNP|_ named|name|VBD|_ RNA23|RNA23|NNP|_ Rocket|Rocket|NNP|_
Using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ an|a|DT|_ EPEC|epec|NN|_ O127|o127|NN|_ :|:|:|_ H6|h6|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ EMBL/GenBank|embl/genbank|NN|_ accession|accession|NN|_ codes|code|NNS|_ FM180568|fm180568|NN|_ ,|,|,|_ FM180569|fm180569|NN|_ ,|,|,|_ and|and|CC|_ FM180570|fm180570|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ quality|quality|JJ|_ checked|check|VBN|_ with|with|IN|_ SAMstat|samstat|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 1.08|1.08|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ transcripts|transcript|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ in|in|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ -RRB-|-rrb-|-RRB-|_
Differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ DGE|dge|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ on|on|IN|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ in|in|IN|_ Cufflinks|Cufflinks|NNP|_ '|'|POS|_ Cuffdiff|cuffdiff|JJ|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.0.7|0.0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
DGE|dge|NN|_ analysis|analysis|NN|_ used|use|VBD|_ a|a|DT|_ false-discovery|false-discovery|JJ|_ rate|rate|NN|_ -LRB-|-lrb-|-LRB-|_ FDR|FDR|NNP|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.10|0.10|CD|_ .|.|.|_
Subsequent|subsequent|JJ|_ data|datum|NNS|_ visualizations|visualization|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.2|3.1.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.0|3.0|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180568|fm180568|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180569|fm180569|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180570|fm180570|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ bedgraph|bedgraph|NN|_ :|:|:|_ Data|datum|NNS|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ 4|4|CD|_ column|column|NN|_ BED|bed|NN|_ format|format|NN|_ ,|,|,|_ of|of|IN|_ which|which|WDT|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ chromosome|chromosome|NN|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ start|start|NN|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ chromosome|chromosome|NN|_ ,|,|,|_ the|the|DT|_ third|third|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ end|end|NN|_ position|position|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ fourth|fourth|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ that|that|DT|_ sample|sample|NN|_ .|.|.|_ Chromosome|chromosome|NN|_ positions|position|NNS|_ are|be|VBP|_ specified|specify|VBN|_ as|as|IN|_ 0-relative|0-relative|JJ|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ chromosome|chromosome|NN|_ position|position|NN|_ is|be|VBZ|_ 0|0|CD|_ .|.|.|_ The|the|DT|_ last|last|JJ|_ position|position|NN|_ in|in|IN|_ a|a|DT|_ chromosome|chromosome|NN|_ of|of|IN|_ length|length|NN|_ N|n|NN|_ would|would|MD|_ be|be|VB|_ N|n|NN|_ -|-|:|_ 1|1|CD|_ .|.|.|_ Only|only|RB|_ positions|position|NNS|_ specified|specify|VBN|_ have|have|VBP|_ data|datum|NNS|_ .|.|.|_ Positions|position|NNS|_ not|not|RB|_ specified|specify|VBN|_ do|do|VBP|_ not|not|RB|_ have|have|VB|_ data|datum|NNS|_ and|and|CC|_ will|will|MD|_ not|not|RB|_ be|be|VB|_ graphed|graph|VBN|_ .|.|.|_ All|all|DT|_ positions|position|NNS|_ specified|specify|VBN|_ in|in|IN|_ the|the|DT|_ input|input|NN|_ data|datum|NNS|_ are|be|VBP|_ in|in|IN|_ numerical|numerical|JJ|_ order|order|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tabular|tabular|JJ|_ :|:|:|_ Tabular|tabular|JJ|_ data|datum|NNS|_ that|that|WDT|_ informs|inform|VBZ|_ the|the|DT|_ excel|excel|VB|_ spreadsheet|spreadsheet|NN|_ .|.|.|_ The|the|DT|_ data|datum|NNS|_ are|be|VBP|_ averaged|average|VBN|_ across|across|IN|_ the|the|DT|_ three|three|CD|_ samples|sample|NNS|_ per|per|IN|_ strain|strain|NN|_ .|.|.|_ Both|both|DT|_ averaged|average|VBD|_ strain|strain|NN|_ data|datum|NNS|_ are|be|VBP|_ presented|present|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ on|on|IN|_ the|the|DT|_ same|same|JJ|_ line|line|NN|_ .|.|.|_ Data|datum|NNS|_ contain|contain|VBP|_ gene|gene|NN|_ ID|id|NN|_ ,|,|,|_ gene|gene|NN|_ number|number|NN|_ ,|,|,|_ locus|locus|NN|_ ,|,|,|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ fold-change|fold-change|NN|_ -RRB-|-rrb-|-RRB-|_ relative|relative|JJ|_ epxression|epxression|NN|_ of|of|IN|_ WT|WT|NNP|_ over|over|IN|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ test-statistic|test-statistic|JJ|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ ,|,|,|_ and|and|CC|_ significance|significance|NN|_ analyzed|analyze|VBD|_ via|via|IN|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ whereby|whereby|WRB|_ a|a|DT|_ q-value|q-value|NN|_ of|of|IN|_ <|<|JJR|_ 0.05|0.05|CD|_ is|be|VBZ|_ considered|consider|VBN|_ significant|significant|JJ|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xls|xl|NNS|_ :|:|:|_ The|the|DT|_ data|datum|NNS|_ are|be|VBP|_ averaged|average|VBN|_ across|across|IN|_ the|the|DT|_ three|three|CD|_ samples|sample|NNS|_ per|per|IN|_ strain|strain|NN|_ .|.|.|_ Both|both|DT|_ averaged|average|VBD|_ strain|strain|NN|_ data|datum|NNS|_ are|be|VBP|_ presented|present|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ on|on|IN|_ the|the|DT|_ same|same|JJ|_ line|line|NN|_ .|.|.|_ Excel|Excel|NNP|_ spreadsheet|spreadsheet|NN|_ containing|contain|VBG|_ gene|gene|NN|_ ID|id|NN|_ ,|,|,|_ gene|gene|NN|_ number|number|NN|_ ,|,|,|_ locus|locus|NN|_ ,|,|,|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ fold-change|fold-change|NN|_ -RRB-|-rrb-|-RRB-|_ relative|relative|JJ|_ epxression|epxression|NN|_ of|of|IN|_ WT|WT|NNP|_ over|over|IN|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ test-statistic|test-statistic|JJ|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ ,|,|,|_ and|and|CC|_ significance|significance|NN|_ analyzed|analyze|VBD|_ via|via|IN|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ whereby|whereby|WRB|_ a|a|DT|_ q-value|q-value|NN|_ of|of|IN|_ <|<|JJR|_ 0.05|0.05|CD|_ is|be|VBZ|_ considered|consider|VBN|_ significant|significant|JJ|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:1|1:1|CD|_ in|in|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ inhibit|inhibit|VB|_ RNase|rnase|NN|_ activity|activity|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ -LRB-|-lrb-|-LRB-|_ 5000|5000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TE/lysozyme|te/lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ ,|,|,|_ 0.5|0.5|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ added|add|VBN|_ proteinase|proteinase|NN|_ K|k|NN|_ -LRB-|-lrb-|-LRB-|_ 1.5|1.5|CD|_ mg/ml|mg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ instructions|instruction|NNS|_ with|with|IN|_ slight|slight|JJ|_ modification|modification|NN|_ .|.|.|_ Before|before|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ buffer|buffer|NN|_ RLT|rlt|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Additionally|additionally|RB|_ ,|,|,|_ during|during|IN|_ the|the|DT|_ wash|wash|NN|_ step|step|NN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ buffer|buffer|NN|_ RDD|rdd|NN|_ -LRB-|-lrb-|-LRB-|_ 310|310|CD|_ Kunitz|Kunitz|NNP|_ units/mL|units/ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ added|add|VBD|_ to|to|TO|_ the|the|DT|_ purification|purification|NN|_ column|column|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ isolation|isolation|NN|_ ,|,|,|_ spectrophotometric|spectrophotometric|JJ|_ NanoDrop|NanoDrop|NNP|_ -LRB-|-lrb-|-LRB-|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ v3|v3|NN|_ .8.1|.8.1|CD|_ ;|;|:|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ -RRB-|-rrb-|-RRB-|_ curves|curve|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ for|for|IN|_ each|each|DT|_ total|total|JJ|_ RNA|rna|NN|_ sample|sample|NN|_ and|and|CC|_ verified|verify|VBN|_ for|for|IN|_ purity|purity|NN|_ ,|,|,|_ as|as|IN|_ defined|define|VBN|_ by|by|IN|_ absorbance|absorbance|NN|_ ratios|ratio|NNS|_ at|at|IN|_ 260/280|260/280|CD|_ nm|nm|NN|_ and|and|CC|_ 260/230|260/230|CD|_ nm|nm|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ Oregon|Oregon|NNP|_ State|State|NNP|_ University|University|NNP|_ 's|'s|POS|_ Center|Center|NNP|_ for|for|IN|_ Genome|Genome|NNP|_ Research|Research|NNP|_ and|and|CC|_ Biocomputing|Biocomputing|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ -LRB-|-lrb-|-LRB-|_ RIN|rin|NN|_ -RRB-|-rrb-|-RRB-|_ measurements|measurement|NNS|_ were|be|VBD|_ taken|take|VBN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ ,|,|,|_ resulting|result|VBG|_ in|in|IN|_ RIN|RIN|NNP|_ scores|score|NNS|_ of|of|IN|_ 10|10|CD|_ ,|,|,|_ out|out|IN|_ of|of|IN|_ a|a|DT|_ possible|possible|JJ|_ 10|10|CD|_ ,|,|,|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Eugene|Eugene|NNP|_ ,|,|,|_ OR|or|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Resulting|result|VBG|_ mRNA|mrna|NN|_ was|be|VBD|_ reverse-transcribed|reverse-transcribed|JJ|_ to|to|TO|_ cDNA|cdna|NN|_ libraries|library|NNS|_ via|via|IN|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ reverse|reverse|VB|_ transcription|transcription|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ 18080051|18080051|CD|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ multiplexed|multiplex|VBN|_ to|to|TO|_ distinguish|distinguish|VB|_ replicates|replicate|VBZ|_ from|from|IN|_ one|one|CD|_ another|another|DT|_ ,|,|,|_ barcoded|barcode|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ for|for|IN|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ .|.|.|_ Transcripts|transcript|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ for|for|IN|_ 50|50|CD|_ bases|basis|NNS|_ in|in|IN|_ single-end|single-end|JJ|_ fashion|fashion|NN|_ within|within|IN|_ one|one|CD|_ lane|lane|NN|_ of|of|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Hiseq|Hiseq|NNP|_ 2000|2000|CD|_ flow|flow|NN|_ cell|cell|NN|_ .|.|.|_ This|this|DT|_ yielded|yield|VBD|_ roughly|roughly|RB|_ 30|30|CD|_ million|million|CD|_ reads|read|VBZ|_ per|per|IN|_ sample|sample|NN|_ .|.|.|_
LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ inoculated|inoculate|VBN|_ by|by|IN|_ a|a|DT|_ frozen|frozen|JJ|_ stock|stock|NN|_ of|of|IN|_ WT|WT|NNP|_ or|or|CC|_ perC-mutant|perc-mutant|JJ|_ strain|strain|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ .|.|.|_ Flasks|flask|NNS|_ containing|contain|VBG|_ low-glucose|low-glucose|JJ|_ DMEM|dmem|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ 1:100|1:100|CD|_ with|with|IN|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 0.3-0.5|0.3-0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Whole|whole|JJ|_ bacterial|bacterial|JJ|_ cell|cell|NN|_ RNA|rna|NN|_ transcriptome|transcriptome|NN|_
Incubation|incubation|NN|_ and|and|CC|_ RNA|rna|NN|_ harvesting|harvesting|NN|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ for|for|IN|_ all|all|DT|_ samples|sample|NNS|_ simultaneously|simultaneously|RB|_ and|and|CC|_ under|under|IN|_ RNase-free|rnase-free|JJ|_ conditions|condition|NNS|_ to|to|TO|_ minimize|minimize|VB|_ biological|biological|JJ|_ variability|variability|NN|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Bacterial|bacterial|JJ|_ concentrations|concentration|NNS|_ were|be|VBD|_ equalized|equalize|VBN|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ by|by|IN|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ JPEP22|jpep22|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ perC|perc|NN|_ :|:|:|_ :|:|:|_ kanR|kanr|NN|_ ,|,|,|_ coisogenic|coisogenic|JJ|_ to|to|TO|_ WT|wt|JJ|_
source|source|NN|_ :|:|:|_ Bustamante|Bustamante|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_
LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ inoculated|inoculate|VBN|_ by|by|IN|_ a|a|DT|_ frozen|frozen|JJ|_ stock|stock|NN|_ of|of|IN|_ WT|WT|NNP|_ or|or|CC|_ perC-mutant|perc-mutant|JJ|_ strain|strain|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ .|.|.|_ Flasks|flask|NNS|_ containing|contain|VBG|_ low-glucose|low-glucose|JJ|_ DMEM|dmem|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ 1:100|1:100|CD|_ with|with|IN|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 0.3-0.5|0.3-0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Whole|whole|JJ|_ bacterial|bacterial|JJ|_ cell|cell|NN|_ RNA|rna|NN|_ transcriptome|transcriptome|NN|_
Incubation|incubation|NN|_ and|and|CC|_ RNA|rna|NN|_ harvesting|harvesting|NN|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ for|for|IN|_ all|all|DT|_ samples|sample|NNS|_ simultaneously|simultaneously|RB|_ and|and|CC|_ under|under|IN|_ RNase-free|rnase-free|JJ|_ conditions|condition|NNS|_ to|to|TO|_ minimize|minimize|VB|_ biological|biological|JJ|_ variability|variability|NN|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Bacterial|bacterial|JJ|_ concentrations|concentration|NNS|_ were|be|VBD|_ equalized|equalize|VBN|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ by|by|IN|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Jay|Jay|NNP|_ ,|,|,|_ ,|,|,|_ Mellies|Mellies|NNP|_
For|for|IN|_ the|the|DT|_ whole-transcriptome|whole-transcriptome|JJ|_ analysis|analysis|NN|_ ,|,|,|_ sequencing|sequencing|NN|_ was|be|VBD|_ verified|verify|VBN|_ using|use|VBG|_ FASTQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.11.2|0.11.2|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ confirm|confirm|VB|_ base-call|base-call|JJ|_ quality|quality|NN|_ in|in|IN|_ each|each|DT|_ indexed|index|VBN|_ file|file|NN|_ .|.|.|_
Indices|Indices|NNPS|_ corresponding|correspond|VBG|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ were|be|VBD|_ merged|merge|VBN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ uploaded|upload|VBD|_ to|to|TO|_ a|a|DT|_ cloud-based|cloud-based|JJ|_ variant|variant|NN|_ of|of|IN|_ Galaxy|Galaxy|NNP|_ named|name|VBD|_ RNA23|RNA23|NNP|_ Rocket|Rocket|NNP|_
Using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ an|a|DT|_ EPEC|epec|NN|_ O127|o127|NN|_ :|:|:|_ H6|h6|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ EMBL/GenBank|embl/genbank|NN|_ accession|accession|NN|_ codes|code|NNS|_ FM180568|fm180568|NN|_ ,|,|,|_ FM180569|fm180569|NN|_ ,|,|,|_ and|and|CC|_ FM180570|fm180570|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ quality|quality|JJ|_ checked|check|VBN|_ with|with|IN|_ SAMstat|samstat|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 1.08|1.08|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ transcripts|transcript|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ in|in|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ -RRB-|-rrb-|-RRB-|_
Differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ DGE|dge|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ on|on|IN|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ in|in|IN|_ Cufflinks|Cufflinks|NNP|_ '|'|POS|_ Cuffdiff|cuffdiff|JJ|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.0.7|0.0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
DGE|dge|NN|_ analysis|analysis|NN|_ used|use|VBD|_ a|a|DT|_ false-discovery|false-discovery|JJ|_ rate|rate|NN|_ -LRB-|-lrb-|-LRB-|_ FDR|FDR|NNP|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.10|0.10|CD|_ .|.|.|_
Subsequent|subsequent|JJ|_ data|datum|NNS|_ visualizations|visualization|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.2|3.1.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.0|3.0|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180568|fm180568|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180569|fm180569|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180570|fm180570|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ bedgraph|bedgraph|NN|_ :|:|:|_ Data|datum|NNS|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ 4|4|CD|_ column|column|NN|_ BED|bed|NN|_ format|format|NN|_ ,|,|,|_ of|of|IN|_ which|which|WDT|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ chromosome|chromosome|NN|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ start|start|NN|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ chromosome|chromosome|NN|_ ,|,|,|_ the|the|DT|_ third|third|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ end|end|NN|_ position|position|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ fourth|fourth|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ that|that|DT|_ sample|sample|NN|_ .|.|.|_ Chromosome|chromosome|NN|_ positions|position|NNS|_ are|be|VBP|_ specified|specify|VBN|_ as|as|IN|_ 0-relative|0-relative|JJ|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ chromosome|chromosome|NN|_ position|position|NN|_ is|be|VBZ|_ 0|0|CD|_ .|.|.|_ The|the|DT|_ last|last|JJ|_ position|position|NN|_ in|in|IN|_ a|a|DT|_ chromosome|chromosome|NN|_ of|of|IN|_ length|length|NN|_ N|n|NN|_ would|would|MD|_ be|be|VB|_ N|n|NN|_ -|-|:|_ 1|1|CD|_ .|.|.|_ Only|only|RB|_ positions|position|NNS|_ specified|specify|VBN|_ have|have|VBP|_ data|datum|NNS|_ .|.|.|_ Positions|position|NNS|_ not|not|RB|_ specified|specify|VBN|_ do|do|VBP|_ not|not|RB|_ have|have|VB|_ data|datum|NNS|_ and|and|CC|_ will|will|MD|_ not|not|RB|_ be|be|VB|_ graphed|graph|VBN|_ .|.|.|_ All|all|DT|_ positions|position|NNS|_ specified|specify|VBN|_ in|in|IN|_ the|the|DT|_ input|input|NN|_ data|datum|NNS|_ are|be|VBP|_ in|in|IN|_ numerical|numerical|JJ|_ order|order|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tabular|tabular|JJ|_ :|:|:|_ Tabular|tabular|JJ|_ data|datum|NNS|_ that|that|WDT|_ informs|inform|VBZ|_ the|the|DT|_ excel|excel|VB|_ spreadsheet|spreadsheet|NN|_ .|.|.|_ The|the|DT|_ data|datum|NNS|_ are|be|VBP|_ averaged|average|VBN|_ across|across|IN|_ the|the|DT|_ three|three|CD|_ samples|sample|NNS|_ per|per|IN|_ strain|strain|NN|_ .|.|.|_ Both|both|DT|_ averaged|average|VBD|_ strain|strain|NN|_ data|datum|NNS|_ are|be|VBP|_ presented|present|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ on|on|IN|_ the|the|DT|_ same|same|JJ|_ line|line|NN|_ .|.|.|_ Data|datum|NNS|_ contain|contain|VBP|_ gene|gene|NN|_ ID|id|NN|_ ,|,|,|_ gene|gene|NN|_ number|number|NN|_ ,|,|,|_ locus|locus|NN|_ ,|,|,|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ fold-change|fold-change|NN|_ -RRB-|-rrb-|-RRB-|_ relative|relative|JJ|_ epxression|epxression|NN|_ of|of|IN|_ WT|WT|NNP|_ over|over|IN|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ test-statistic|test-statistic|JJ|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ ,|,|,|_ and|and|CC|_ significance|significance|NN|_ analyzed|analyze|VBD|_ via|via|IN|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ whereby|whereby|WRB|_ a|a|DT|_ q-value|q-value|NN|_ of|of|IN|_ <|<|JJR|_ 0.05|0.05|CD|_ is|be|VBZ|_ considered|consider|VBN|_ significant|significant|JJ|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xls|xl|NNS|_ :|:|:|_ The|the|DT|_ data|datum|NNS|_ are|be|VBP|_ averaged|average|VBN|_ across|across|IN|_ the|the|DT|_ three|three|CD|_ samples|sample|NNS|_ per|per|IN|_ strain|strain|NN|_ .|.|.|_ Both|both|DT|_ averaged|average|VBD|_ strain|strain|NN|_ data|datum|NNS|_ are|be|VBP|_ presented|present|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ on|on|IN|_ the|the|DT|_ same|same|JJ|_ line|line|NN|_ .|.|.|_ Excel|Excel|NNP|_ spreadsheet|spreadsheet|NN|_ containing|contain|VBG|_ gene|gene|NN|_ ID|id|NN|_ ,|,|,|_ gene|gene|NN|_ number|number|NN|_ ,|,|,|_ locus|locus|NN|_ ,|,|,|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ fold-change|fold-change|NN|_ -RRB-|-rrb-|-RRB-|_ relative|relative|JJ|_ epxression|epxression|NN|_ of|of|IN|_ WT|WT|NNP|_ over|over|IN|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ test-statistic|test-statistic|JJ|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ ,|,|,|_ and|and|CC|_ significance|significance|NN|_ analyzed|analyze|VBD|_ via|via|IN|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ whereby|whereby|WRB|_ a|a|DT|_ q-value|q-value|NN|_ of|of|IN|_ <|<|JJR|_ 0.05|0.05|CD|_ is|be|VBZ|_ considered|consider|VBN|_ significant|significant|JJ|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:1|1:1|CD|_ in|in|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ inhibit|inhibit|VB|_ RNase|rnase|NN|_ activity|activity|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ -LRB-|-lrb-|-LRB-|_ 5000|5000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TE/lysozyme|te/lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ ,|,|,|_ 0.5|0.5|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ added|add|VBN|_ proteinase|proteinase|NN|_ K|k|NN|_ -LRB-|-lrb-|-LRB-|_ 1.5|1.5|CD|_ mg/ml|mg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ instructions|instruction|NNS|_ with|with|IN|_ slight|slight|JJ|_ modification|modification|NN|_ .|.|.|_ Before|before|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ buffer|buffer|NN|_ RLT|rlt|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Additionally|additionally|RB|_ ,|,|,|_ during|during|IN|_ the|the|DT|_ wash|wash|NN|_ step|step|NN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ buffer|buffer|NN|_ RDD|rdd|NN|_ -LRB-|-lrb-|-LRB-|_ 310|310|CD|_ Kunitz|Kunitz|NNP|_ units/mL|units/ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ added|add|VBD|_ to|to|TO|_ the|the|DT|_ purification|purification|NN|_ column|column|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ isolation|isolation|NN|_ ,|,|,|_ spectrophotometric|spectrophotometric|JJ|_ NanoDrop|NanoDrop|NNP|_ -LRB-|-lrb-|-LRB-|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ v3|v3|NN|_ .8.1|.8.1|CD|_ ;|;|:|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ -RRB-|-rrb-|-RRB-|_ curves|curve|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ for|for|IN|_ each|each|DT|_ total|total|JJ|_ RNA|rna|NN|_ sample|sample|NN|_ and|and|CC|_ verified|verify|VBN|_ for|for|IN|_ purity|purity|NN|_ ,|,|,|_ as|as|IN|_ defined|define|VBN|_ by|by|IN|_ absorbance|absorbance|NN|_ ratios|ratio|NNS|_ at|at|IN|_ 260/280|260/280|CD|_ nm|nm|NN|_ and|and|CC|_ 260/230|260/230|CD|_ nm|nm|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ Oregon|Oregon|NNP|_ State|State|NNP|_ University|University|NNP|_ 's|'s|POS|_ Center|Center|NNP|_ for|for|IN|_ Genome|Genome|NNP|_ Research|Research|NNP|_ and|and|CC|_ Biocomputing|Biocomputing|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ -LRB-|-lrb-|-LRB-|_ RIN|rin|NN|_ -RRB-|-rrb-|-RRB-|_ measurements|measurement|NNS|_ were|be|VBD|_ taken|take|VBN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ ,|,|,|_ resulting|result|VBG|_ in|in|IN|_ RIN|RIN|NNP|_ scores|score|NNS|_ of|of|IN|_ 10|10|CD|_ ,|,|,|_ out|out|IN|_ of|of|IN|_ a|a|DT|_ possible|possible|JJ|_ 10|10|CD|_ ,|,|,|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Eugene|Eugene|NNP|_ ,|,|,|_ OR|or|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Resulting|result|VBG|_ mRNA|mrna|NN|_ was|be|VBD|_ reverse-transcribed|reverse-transcribed|JJ|_ to|to|TO|_ cDNA|cdna|NN|_ libraries|library|NNS|_ via|via|IN|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ reverse|reverse|VB|_ transcription|transcription|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ 18080051|18080051|CD|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ multiplexed|multiplex|VBN|_ to|to|TO|_ distinguish|distinguish|VB|_ replicates|replicate|VBZ|_ from|from|IN|_ one|one|CD|_ another|another|DT|_ ,|,|,|_ barcoded|barcode|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ for|for|IN|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ .|.|.|_ Transcripts|transcript|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ for|for|IN|_ 50|50|CD|_ bases|basis|NNS|_ in|in|IN|_ single-end|single-end|JJ|_ fashion|fashion|NN|_ within|within|IN|_ one|one|CD|_ lane|lane|NN|_ of|of|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Hiseq|Hiseq|NNP|_ 2000|2000|CD|_ flow|flow|NN|_ cell|cell|NN|_ .|.|.|_ This|this|DT|_ yielded|yield|VBD|_ roughly|roughly|RB|_ 30|30|CD|_ million|million|CD|_ reads|read|VBZ|_ per|per|IN|_ sample|sample|NN|_ .|.|.|_
LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ inoculated|inoculate|VBN|_ by|by|IN|_ a|a|DT|_ frozen|frozen|JJ|_ stock|stock|NN|_ of|of|IN|_ WT|WT|NNP|_ or|or|CC|_ perC-mutant|perc-mutant|JJ|_ strain|strain|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ .|.|.|_ Flasks|flask|NNS|_ containing|contain|VBG|_ low-glucose|low-glucose|JJ|_ DMEM|dmem|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ 1:100|1:100|CD|_ with|with|IN|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 0.3-0.5|0.3-0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Whole|whole|JJ|_ bacterial|bacterial|JJ|_ cell|cell|NN|_ RNA|rna|NN|_ transcriptome|transcriptome|NN|_
Incubation|incubation|NN|_ and|and|CC|_ RNA|rna|NN|_ harvesting|harvesting|NN|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ for|for|IN|_ all|all|DT|_ samples|sample|NNS|_ simultaneously|simultaneously|RB|_ and|and|CC|_ under|under|IN|_ RNase-free|rnase-free|JJ|_ conditions|condition|NNS|_ to|to|TO|_ minimize|minimize|VB|_ biological|biological|JJ|_ variability|variability|NN|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Bacterial|bacterial|JJ|_ concentrations|concentration|NNS|_ were|be|VBD|_ equalized|equalize|VBN|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ by|by|IN|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ JPEP22|jpep22|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ perC|perc|NN|_ :|:|:|_ :|:|:|_ kanR|kanr|NN|_ ,|,|,|_ coisogenic|coisogenic|JJ|_ to|to|TO|_ WT|wt|JJ|_
source|source|NN|_ :|:|:|_ Bustamante|Bustamante|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_
LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ inoculated|inoculate|VBN|_ by|by|IN|_ a|a|DT|_ frozen|frozen|JJ|_ stock|stock|NN|_ of|of|IN|_ WT|WT|NNP|_ or|or|CC|_ perC-mutant|perc-mutant|JJ|_ strain|strain|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ .|.|.|_ Flasks|flask|NNS|_ containing|contain|VBG|_ low-glucose|low-glucose|JJ|_ DMEM|dmem|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ 1:100|1:100|CD|_ with|with|IN|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 0.3-0.5|0.3-0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Whole|whole|JJ|_ bacterial|bacterial|JJ|_ cell|cell|NN|_ RNA|rna|NN|_ transcriptome|transcriptome|NN|_
Incubation|incubation|NN|_ and|and|CC|_ RNA|rna|NN|_ harvesting|harvesting|NN|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ for|for|IN|_ all|all|DT|_ samples|sample|NNS|_ simultaneously|simultaneously|RB|_ and|and|CC|_ under|under|IN|_ RNase-free|rnase-free|JJ|_ conditions|condition|NNS|_ to|to|TO|_ minimize|minimize|VB|_ biological|biological|JJ|_ variability|variability|NN|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Bacterial|bacterial|JJ|_ concentrations|concentration|NNS|_ were|be|VBD|_ equalized|equalize|VBN|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ by|by|IN|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Jay|Jay|NNP|_ ,|,|,|_ ,|,|,|_ Mellies|Mellies|NNP|_
For|for|IN|_ the|the|DT|_ whole-transcriptome|whole-transcriptome|JJ|_ analysis|analysis|NN|_ ,|,|,|_ sequencing|sequencing|NN|_ was|be|VBD|_ verified|verify|VBN|_ using|use|VBG|_ FASTQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.11.2|0.11.2|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ confirm|confirm|VB|_ base-call|base-call|JJ|_ quality|quality|NN|_ in|in|IN|_ each|each|DT|_ indexed|index|VBN|_ file|file|NN|_ .|.|.|_
Indices|Indices|NNPS|_ corresponding|correspond|VBG|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ were|be|VBD|_ merged|merge|VBN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ uploaded|upload|VBD|_ to|to|TO|_ a|a|DT|_ cloud-based|cloud-based|JJ|_ variant|variant|NN|_ of|of|IN|_ Galaxy|Galaxy|NNP|_ named|name|VBD|_ RNA23|RNA23|NNP|_ Rocket|Rocket|NNP|_
Using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ an|a|DT|_ EPEC|epec|NN|_ O127|o127|NN|_ :|:|:|_ H6|h6|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ EMBL/GenBank|embl/genbank|NN|_ accession|accession|NN|_ codes|code|NNS|_ FM180568|fm180568|NN|_ ,|,|,|_ FM180569|fm180569|NN|_ ,|,|,|_ and|and|CC|_ FM180570|fm180570|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ quality|quality|JJ|_ checked|check|VBN|_ with|with|IN|_ SAMstat|samstat|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 1.08|1.08|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ transcripts|transcript|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ in|in|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ -RRB-|-rrb-|-RRB-|_
Differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ DGE|dge|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ on|on|IN|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ in|in|IN|_ Cufflinks|Cufflinks|NNP|_ '|'|POS|_ Cuffdiff|cuffdiff|JJ|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.0.7|0.0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
DGE|dge|NN|_ analysis|analysis|NN|_ used|use|VBD|_ a|a|DT|_ false-discovery|false-discovery|JJ|_ rate|rate|NN|_ -LRB-|-lrb-|-LRB-|_ FDR|FDR|NNP|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.10|0.10|CD|_ .|.|.|_
Subsequent|subsequent|JJ|_ data|datum|NNS|_ visualizations|visualization|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.2|3.1.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.0|3.0|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180568|fm180568|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180569|fm180569|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180570|fm180570|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ bedgraph|bedgraph|NN|_ :|:|:|_ Data|datum|NNS|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ 4|4|CD|_ column|column|NN|_ BED|bed|NN|_ format|format|NN|_ ,|,|,|_ of|of|IN|_ which|which|WDT|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ chromosome|chromosome|NN|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ start|start|NN|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ chromosome|chromosome|NN|_ ,|,|,|_ the|the|DT|_ third|third|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ end|end|NN|_ position|position|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ fourth|fourth|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ that|that|DT|_ sample|sample|NN|_ .|.|.|_ Chromosome|chromosome|NN|_ positions|position|NNS|_ are|be|VBP|_ specified|specify|VBN|_ as|as|IN|_ 0-relative|0-relative|JJ|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ chromosome|chromosome|NN|_ position|position|NN|_ is|be|VBZ|_ 0|0|CD|_ .|.|.|_ The|the|DT|_ last|last|JJ|_ position|position|NN|_ in|in|IN|_ a|a|DT|_ chromosome|chromosome|NN|_ of|of|IN|_ length|length|NN|_ N|n|NN|_ would|would|MD|_ be|be|VB|_ N|n|NN|_ -|-|:|_ 1|1|CD|_ .|.|.|_ Only|only|RB|_ positions|position|NNS|_ specified|specify|VBN|_ have|have|VBP|_ data|datum|NNS|_ .|.|.|_ Positions|position|NNS|_ not|not|RB|_ specified|specify|VBN|_ do|do|VBP|_ not|not|RB|_ have|have|VB|_ data|datum|NNS|_ and|and|CC|_ will|will|MD|_ not|not|RB|_ be|be|VB|_ graphed|graph|VBN|_ .|.|.|_ All|all|DT|_ positions|position|NNS|_ specified|specify|VBN|_ in|in|IN|_ the|the|DT|_ input|input|NN|_ data|datum|NNS|_ are|be|VBP|_ in|in|IN|_ numerical|numerical|JJ|_ order|order|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tabular|tabular|JJ|_ :|:|:|_ Tabular|tabular|JJ|_ data|datum|NNS|_ that|that|WDT|_ informs|inform|VBZ|_ the|the|DT|_ excel|excel|VB|_ spreadsheet|spreadsheet|NN|_ .|.|.|_ The|the|DT|_ data|datum|NNS|_ are|be|VBP|_ averaged|average|VBN|_ across|across|IN|_ the|the|DT|_ three|three|CD|_ samples|sample|NNS|_ per|per|IN|_ strain|strain|NN|_ .|.|.|_ Both|both|DT|_ averaged|average|VBD|_ strain|strain|NN|_ data|datum|NNS|_ are|be|VBP|_ presented|present|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ on|on|IN|_ the|the|DT|_ same|same|JJ|_ line|line|NN|_ .|.|.|_ Data|datum|NNS|_ contain|contain|VBP|_ gene|gene|NN|_ ID|id|NN|_ ,|,|,|_ gene|gene|NN|_ number|number|NN|_ ,|,|,|_ locus|locus|NN|_ ,|,|,|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ fold-change|fold-change|NN|_ -RRB-|-rrb-|-RRB-|_ relative|relative|JJ|_ epxression|epxression|NN|_ of|of|IN|_ WT|WT|NNP|_ over|over|IN|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ test-statistic|test-statistic|JJ|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ ,|,|,|_ and|and|CC|_ significance|significance|NN|_ analyzed|analyze|VBD|_ via|via|IN|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ whereby|whereby|WRB|_ a|a|DT|_ q-value|q-value|NN|_ of|of|IN|_ <|<|JJR|_ 0.05|0.05|CD|_ is|be|VBZ|_ considered|consider|VBN|_ significant|significant|JJ|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xls|xl|NNS|_ :|:|:|_ The|the|DT|_ data|datum|NNS|_ are|be|VBP|_ averaged|average|VBN|_ across|across|IN|_ the|the|DT|_ three|three|CD|_ samples|sample|NNS|_ per|per|IN|_ strain|strain|NN|_ .|.|.|_ Both|both|DT|_ averaged|average|VBD|_ strain|strain|NN|_ data|datum|NNS|_ are|be|VBP|_ presented|present|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ on|on|IN|_ the|the|DT|_ same|same|JJ|_ line|line|NN|_ .|.|.|_ Excel|Excel|NNP|_ spreadsheet|spreadsheet|NN|_ containing|contain|VBG|_ gene|gene|NN|_ ID|id|NN|_ ,|,|,|_ gene|gene|NN|_ number|number|NN|_ ,|,|,|_ locus|locus|NN|_ ,|,|,|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ fold-change|fold-change|NN|_ -RRB-|-rrb-|-RRB-|_ relative|relative|JJ|_ epxression|epxression|NN|_ of|of|IN|_ WT|WT|NNP|_ over|over|IN|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ test-statistic|test-statistic|JJ|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ ,|,|,|_ and|and|CC|_ significance|significance|NN|_ analyzed|analyze|VBD|_ via|via|IN|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ whereby|whereby|WRB|_ a|a|DT|_ q-value|q-value|NN|_ of|of|IN|_ <|<|JJR|_ 0.05|0.05|CD|_ is|be|VBZ|_ considered|consider|VBN|_ significant|significant|JJ|_ .|.|.|_
Samples|sample|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:1|1:1|CD|_ in|in|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ inhibit|inhibit|VB|_ RNase|rnase|NN|_ activity|activity|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ -LRB-|-lrb-|-LRB-|_ 5000|5000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TE/lysozyme|te/lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mg/ml|mg/ml|NN|_ lysozyme|lysozyme|NN|_ ,|,|,|_ 0.5|0.5|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ added|add|VBN|_ proteinase|proteinase|NN|_ K|k|NN|_ -LRB-|-lrb-|-LRB-|_ 1.5|1.5|CD|_ mg/ml|mg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ instructions|instruction|NNS|_ with|with|IN|_ slight|slight|JJ|_ modification|modification|NN|_ .|.|.|_ Before|before|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ buffer|buffer|NN|_ RLT|rlt|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Additionally|additionally|RB|_ ,|,|,|_ during|during|IN|_ the|the|DT|_ wash|wash|NN|_ step|step|NN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ buffer|buffer|NN|_ RDD|rdd|NN|_ -LRB-|-lrb-|-LRB-|_ 310|310|CD|_ Kunitz|Kunitz|NNP|_ units/mL|units/ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ added|add|VBD|_ to|to|TO|_ the|the|DT|_ purification|purification|NN|_ column|column|NN|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ isolation|isolation|NN|_ ,|,|,|_ spectrophotometric|spectrophotometric|JJ|_ NanoDrop|NanoDrop|NNP|_ -LRB-|-lrb-|-LRB-|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ v3|v3|NN|_ .8.1|.8.1|CD|_ ;|;|:|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ -RRB-|-rrb-|-RRB-|_ curves|curve|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ for|for|IN|_ each|each|DT|_ total|total|JJ|_ RNA|rna|NN|_ sample|sample|NN|_ and|and|CC|_ verified|verify|VBN|_ for|for|IN|_ purity|purity|NN|_ ,|,|,|_ as|as|IN|_ defined|define|VBN|_ by|by|IN|_ absorbance|absorbance|NN|_ ratios|ratio|NNS|_ at|at|IN|_ 260/280|260/280|CD|_ nm|nm|NN|_ and|and|CC|_ 260/230|260/230|CD|_ nm|nm|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ Oregon|Oregon|NNP|_ State|State|NNP|_ University|University|NNP|_ 's|'s|POS|_ Center|Center|NNP|_ for|for|IN|_ Genome|Genome|NNP|_ Research|Research|NNP|_ and|and|CC|_ Biocomputing|Biocomputing|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ -LRB-|-lrb-|-LRB-|_ RIN|rin|NN|_ -RRB-|-rrb-|-RRB-|_ measurements|measurement|NNS|_ were|be|VBD|_ taken|take|VBN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ ,|,|,|_ resulting|result|VBG|_ in|in|IN|_ RIN|RIN|NNP|_ scores|score|NNS|_ of|of|IN|_ 10|10|CD|_ ,|,|,|_ out|out|IN|_ of|of|IN|_ a|a|DT|_ possible|possible|JJ|_ 10|10|CD|_ ,|,|,|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Eugene|Eugene|NNP|_ ,|,|,|_ OR|or|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Resulting|result|VBG|_ mRNA|mrna|NN|_ was|be|VBD|_ reverse-transcribed|reverse-transcribed|JJ|_ to|to|TO|_ cDNA|cdna|NN|_ libraries|library|NNS|_ via|via|IN|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ reverse|reverse|VB|_ transcription|transcription|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ 18080051|18080051|CD|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ multiplexed|multiplex|VBN|_ to|to|TO|_ distinguish|distinguish|VB|_ replicates|replicate|VBZ|_ from|from|IN|_ one|one|CD|_ another|another|DT|_ ,|,|,|_ barcoded|barcode|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ for|for|IN|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ .|.|.|_ Transcripts|transcript|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ for|for|IN|_ 50|50|CD|_ bases|basis|NNS|_ in|in|IN|_ single-end|single-end|JJ|_ fashion|fashion|NN|_ within|within|IN|_ one|one|CD|_ lane|lane|NN|_ of|of|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Hiseq|Hiseq|NNP|_ 2000|2000|CD|_ flow|flow|NN|_ cell|cell|NN|_ .|.|.|_ This|this|DT|_ yielded|yield|VBD|_ roughly|roughly|RB|_ 30|30|CD|_ million|million|CD|_ reads|read|VBZ|_ per|per|IN|_ sample|sample|NN|_ .|.|.|_
LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ inoculated|inoculate|VBN|_ by|by|IN|_ a|a|DT|_ frozen|frozen|JJ|_ stock|stock|NN|_ of|of|IN|_ WT|WT|NNP|_ or|or|CC|_ perC-mutant|perc-mutant|JJ|_ strain|strain|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ .|.|.|_ Flasks|flask|NNS|_ containing|contain|VBG|_ low-glucose|low-glucose|JJ|_ DMEM|dmem|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ 1:100|1:100|CD|_ with|with|IN|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 0.3-0.5|0.3-0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Whole|whole|JJ|_ bacterial|bacterial|JJ|_ cell|cell|NN|_ RNA|rna|NN|_ transcriptome|transcriptome|NN|_
Incubation|incubation|NN|_ and|and|CC|_ RNA|rna|NN|_ harvesting|harvesting|NN|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ for|for|IN|_ all|all|DT|_ samples|sample|NNS|_ simultaneously|simultaneously|RB|_ and|and|CC|_ under|under|IN|_ RNase-free|rnase-free|JJ|_ conditions|condition|NNS|_ to|to|TO|_ minimize|minimize|VB|_ biological|biological|JJ|_ variability|variability|NN|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Bacterial|bacterial|JJ|_ concentrations|concentration|NNS|_ were|be|VBD|_ equalized|equalize|VBN|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ by|by|IN|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ JPEP22|jpep22|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ perC|perc|NN|_ :|:|:|_ :|:|:|_ kanR|kanr|NN|_ ,|,|,|_ coisogenic|coisogenic|JJ|_ to|to|TO|_ WT|wt|JJ|_
source|source|NN|_ :|:|:|_ Bustamante|Bustamante|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_
LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ inoculated|inoculate|VBN|_ by|by|IN|_ a|a|DT|_ frozen|frozen|JJ|_ stock|stock|NN|_ of|of|IN|_ WT|WT|NNP|_ or|or|CC|_ perC-mutant|perc-mutant|JJ|_ strain|strain|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ .|.|.|_ Flasks|flask|NNS|_ containing|contain|VBG|_ low-glucose|low-glucose|JJ|_ DMEM|dmem|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ 1:100|1:100|CD|_ with|with|IN|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 0.3-0.5|0.3-0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Whole|whole|JJ|_ bacterial|bacterial|JJ|_ cell|cell|NN|_ RNA|rna|NN|_ transcriptome|transcriptome|NN|_
Incubation|incubation|NN|_ and|and|CC|_ RNA|rna|NN|_ harvesting|harvesting|NN|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ for|for|IN|_ all|all|DT|_ samples|sample|NNS|_ simultaneously|simultaneously|RB|_ and|and|CC|_ under|under|IN|_ RNase-free|rnase-free|JJ|_ conditions|condition|NNS|_ to|to|TO|_ minimize|minimize|VB|_ biological|biological|JJ|_ variability|variability|NN|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Bacterial|bacterial|JJ|_ concentrations|concentration|NNS|_ were|be|VBD|_ equalized|equalize|VBN|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ by|by|IN|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Jay|Jay|NNP|_ ,|,|,|_ ,|,|,|_ Mellies|Mellies|NNP|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
TruSeq|truseq|NN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pORF1|porf1|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
induction|induction|NN|_ :|:|:|_ induced|induce|VBN|_ 50|50|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
replicates|replicate|VBZ|_ :|:|:|_ ORF1|orf1|NN|_ replicate|replicate|VB|_ 1|1|CD|_ /|/|:|_ induced|induce|VBN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pORF1|porf1|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Dan|Dan|NNP|_ ,|,|,|_ I.|I.|NNP|_ ,|,|,|_ Andersson|Andersson|NNP|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
TruSeq|truseq|NN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pORF1|porf1|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
replicates|replicate|VBZ|_ :|:|:|_ ORF1|orf1|NN|_ replicate|replicate|VB|_ 1|1|CD|_ /|/|:|_ not|not|RB|_ induced|induce|VBN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pORF1|porf1|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Dan|Dan|NNP|_ ,|,|,|_ I.|I.|NNP|_ ,|,|,|_ Andersson|Andersson|NNP|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
TruSeq|truseq|NN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pORF1|porf1|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
induction|induction|NN|_ :|:|:|_ induced|induce|VBN|_ 50|50|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
replicates|replicate|VBZ|_ :|:|:|_ ORF1|orf1|NN|_ replicate|replicate|VB|_ 2|2|CD|_ /|/|:|_ induced|induce|VBN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pORF1|porf1|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Dan|Dan|NNP|_ ,|,|,|_ I.|I.|NNP|_ ,|,|,|_ Andersson|Andersson|NNP|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
TruSeq|truseq|NN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pORF1|porf1|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
replicates|replicate|VBZ|_ :|:|:|_ ORF1|orf1|NN|_ replicate|replicate|VB|_ 2|2|CD|_ /|/|:|_ not|not|RB|_ induced|induce|VBN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pORF1|porf1|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Dan|Dan|NNP|_ ,|,|,|_ I.|I.|NNP|_ ,|,|,|_ Andersson|Andersson|NNP|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
TruSeq|truseq|NN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
induction|induction|NN|_ :|:|:|_ induced|induce|VBN|_ 50|50|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
replicates|replicate|VBZ|_ :|:|:|_ Svi3-3|svi3-3|NN|_ replicate|replicate|VB|_ 1|1|CD|_ /|/|:|_ induced|induce|VBN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Dan|Dan|NNP|_ ,|,|,|_ I.|I.|NNP|_ ,|,|,|_ Andersson|Andersson|NNP|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
TruSeq|truseq|NN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
replicates|replicate|VBZ|_ :|:|:|_ Svi3-3|svi3-3|NN|_ replicate|replicate|VB|_ 1|1|CD|_ /|/|:|_ not|not|RB|_ induced|induce|VBN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Dan|Dan|NNP|_ ,|,|,|_ I.|I.|NNP|_ ,|,|,|_ Andersson|Andersson|NNP|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
TruSeq|truseq|NN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
induction|induction|NN|_ :|:|:|_ induced|induce|VBN|_ 50|50|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
replicates|replicate|VBZ|_ :|:|:|_ Svi3-3|svi3-3|NN|_ replicate|replicate|VB|_ 2|2|CD|_ /|/|:|_ induced|induce|VBN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Dan|Dan|NNP|_ ,|,|,|_ I.|I.|NNP|_ ,|,|,|_ Andersson|Andersson|NNP|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
TruSeq|truseq|NN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
replicates|replicate|VBZ|_ :|:|:|_ Svi3-3|svi3-3|NN|_ replicate|replicate|VB|_ 2|2|CD|_ /|/|:|_ not|not|RB|_ induced|induce|VBN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Dan|Dan|NNP|_ ,|,|,|_ I.|I.|NNP|_ ,|,|,|_ Andersson|Andersson|NNP|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
TruSeq|truseq|NN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pCA24N|pca24n|NN|_ ,|,|,|_ -|-|:|_ gfp|gfp|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
induction|induction|NN|_ :|:|:|_ induced|induce|VBN|_ 50|50|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
replicates|replicate|VBZ|_ :|:|:|_ WT|WT|NNP|_ replicate|replicate|VB|_ 1|1|CD|_ /|/|:|_ induced|induce|VBN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pCA24N|pca24n|NN|_ ,|,|,|_ -|-|:|_ gfp|gfp|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Dan|Dan|NNP|_ ,|,|,|_ I.|I.|NNP|_ ,|,|,|_ Andersson|Andersson|NNP|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
TruSeq|truseq|NN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pCA24N|pca24n|NN|_ ,|,|,|_ -|-|:|_ gfp|gfp|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
induction|induction|NN|_ :|:|:|_ induced|induce|VBN|_ 50|50|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
replicates|replicate|VBZ|_ :|:|:|_ WT|WT|NNP|_ replicate|replicate|VB|_ 2|2|CD|_ /|/|:|_ induced|induce|VBN|_
Duplicate|duplicate|VB|_ O/N|o/n|NN|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ 15|15|CD|_ mg/L|mg/l|NN|_ chloramphenicol|chloramphenicol|NN|_ each|each|DT|_ of|of|IN|_ strains|strain|NNS|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ ,|,|,|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ two|two|CD|_ ,|,|,|_ four|four|CD|_ and|and|CC|_ four|four|CD|_ cultures|culture|NNS|_ of|of|IN|_ 20|20|CD|_ mL|ml|NN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 5|5|CD|_ μg/mL|μg/ml|NN|_ chloramphenicol|chloramphenicol|NN|_ .|.|.|_ The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ /|/|:|_ pCA24N|pca24n|NN|_ ,|,|,|_ -|-|:|_ gfp|gfp|NN|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_ /|/|:|_ DA4201|da4201|NN|_ cultures|culture|NNS|_ and|and|CC|_ two|two|CD|_ cultures|culture|NNS|_ each|each|DT|_ of|of|IN|_ Svi3-3|svi3-3|NN|_ comp|comp|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ Svi3-3|svi3-3|NN|_ -RRB-|-rrb-|-RRB-|_ /|/|:|_ DA4201|da4201|NN|_ and|and|CC|_ pORF1/DA4201|porf1/da4201|NN|_ were|be|VBD|_ supplemented|supplement|VBN|_ by|by|IN|_ 50|50|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ 0.15-0.2|0.15-0.2|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ and|and|CC|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ .|.|.|_
Dan|Dan|NNP|_ ,|,|,|_ I.|I.|NNP|_ ,|,|,|_ Andersson|Andersson|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 0|0|CD|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 0|0|CD|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 5|5|CD|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 5|5|CD|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|Carolacton|NNP|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 5|5|CD|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|Carolacton|NNP|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 5|5|CD|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 15|15|CD|_
E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 15|15|CD|_
E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|Carolacton|NNP|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 15|15|CD|_
E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|Carolacton|NNP|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 15|15|CD|_
E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 30|30|CD|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 30|30|CD|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|Carolacton|NNP|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 30|30|CD|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
Sequenced|Sequenced|NNP|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
Total|Total|NNP|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Libraries|Libraries|NNPS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|Carolacton|NNP|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 30|30|CD|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o/n|o/n|RB|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
planktonic|planktonic|JJ|_ cells|cell|NNS|_
An|a|DT|_ o/n|o/n|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ TolC|tolc|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.1|0.1|CD|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ µg/ml|µg/ml|NN|_ Carolacton|carolacton|NN|_ in|in|IN|_ MeOH|meoh|NN|_ .|.|.|_ Controls|Controls|NNP|_ received|receive|VBD|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ MeOH|meoh|NN|_ .|.|.|_ Three|three|CD|_ early|early|JJ|_ time-points|time-point|NNS|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ chosen|choose|VBN|_ to|to|TO|_ be|be|VB|_ analyzed|analyze|VBN|_ by|by|IN|_ RNA-seq|rna-seq|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ Carolacton|carolacton|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ t5|t5|NN|_ ,|,|,|_ t15|t15|NN|_ and|and|CC|_ t30|t30|NN|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ Carolacton|Carolacton|NNP|_ .|.|.|_ At|at|IN|_ each|each|DT|_ point|point|NN|_ ,|,|,|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ the|the|DT|_ cells|cell|NNS|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Jannik|Jannik|NNP|_ ,|,|,|_ ,|,|,|_ Donner|Donner|NNP|_
RNA-Seq|rna-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ done|do|VBN|_ using|use|VBG|_ blind|blind|JJ|_ and|and|CC|_ fit-only|fit-only|JJ|_ parameter|parameter|NN|_ in|in|IN|_ DE-Seq|de-seq|NN|_ pakage|pakage|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ FASTX-Toolkit|fastx-toolkit|NN|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ and|and|CC|_ Perl|Perl|NNP|_ version|version|NN|_ 5.8.8|5.8.8|CD|_
first|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ the|the|DT|_ use|use|NN|_ of|of|IN|_ SuperScriptII|superscriptii|NN|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ done|do|VBN|_ before|before|IN|_ end-pair|end-pair|JJ|_ and|and|CC|_ dA-tailing|da-tailing|JJ|_
Reads|read|VBZ|_ longer|longer|JJR|_ than|than|IN|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ ≤|≤|NN|_ 2|2|CD|_ N|n|NN|_ -LRB-|-lrb-|-LRB-|_ ambiguous|ambiguous|JJ|_ nucleotides|nucleotide|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ preserved|preserve|VBN|_ .|.|.|_
Using|use|VBG|_ blind|blind|JJ|_ and|and|CC|_ fit-only|fit-only|JJ|_ parameter|parameter|NN|_ in|in|IN|_ DE-Seq|de-seq|NN|_ pakage|pakage|NN|_ ,|,|,|_ expressions|expression|NNS|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ samples|sample|NNS|_ were|be|VBD|_ changed|change|VBN|_ to|to|TO|_ count|count|VB|_ per|per|IN|_ gene|gene|NN|_ ,|,|,|_ using|use|VBG|_ RNA-Seq|rna-seq|NN|_ protocol|protocol|NN|_ on|on|IN|_ Illumina|Illumina|NNP|_ HiSeq2500|HiSeq2500|NNP|_ platform|platform|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ UCSC|UCSC|NNP|_ mm10|mm10|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ and|and|CC|_ raw|raw|JJ|_ fragment|fragment|NN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ isolates|isolate|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_
Following|follow|VBG|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ TruSeq|truseq|NN|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|Preparation|NNP|_ Guide|Guide|NNP|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Strains|strain|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ MH|mh|NN|_ broth|broth|NN|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Human|human|JJ|_
No|no|DT|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 25922|25922|CD|_
Strains|strain|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ MH|mh|NN|_ broth|broth|NN|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Human|human|JJ|_
No|no|DT|_ treatment|treatment|NN|_
Ganlin|ganlin|NN|_ ,|,|,|_ ,|,|,|_ Xu|Xu|NNP|_
RNA-Seq|rna-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ done|do|VBN|_ using|use|VBG|_ blind|blind|JJ|_ and|and|CC|_ fit-only|fit-only|JJ|_ parameter|parameter|NN|_ in|in|IN|_ DE-Seq|de-seq|NN|_ pakage|pakage|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ FASTX-Toolkit|fastx-toolkit|NN|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ and|and|CC|_ Perl|Perl|NNP|_ version|version|NN|_ 5.8.8|5.8.8|CD|_
first|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ the|the|DT|_ use|use|NN|_ of|of|IN|_ SuperScriptII|superscriptii|NN|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ done|do|VBN|_ before|before|IN|_ end-pair|end-pair|JJ|_ and|and|CC|_ dA-tailing|da-tailing|JJ|_
Reads|read|VBZ|_ longer|longer|JJR|_ than|than|IN|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ ≤|≤|NN|_ 2|2|CD|_ N|n|NN|_ -LRB-|-lrb-|-LRB-|_ ambiguous|ambiguous|JJ|_ nucleotides|nucleotide|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ preserved|preserve|VBN|_ .|.|.|_
Using|use|VBG|_ blind|blind|JJ|_ and|and|CC|_ fit-only|fit-only|JJ|_ parameter|parameter|NN|_ in|in|IN|_ DE-Seq|de-seq|NN|_ pakage|pakage|NN|_ ,|,|,|_ expressions|expression|NNS|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ samples|sample|NNS|_ were|be|VBD|_ changed|change|VBN|_ to|to|TO|_ count|count|VB|_ per|per|IN|_ gene|gene|NN|_ ,|,|,|_ using|use|VBG|_ RNA-Seq|rna-seq|NN|_ protocol|protocol|NN|_ on|on|IN|_ Illumina|Illumina|NNP|_ HiSeq2500|HiSeq2500|NNP|_ platform|platform|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ UCSC|UCSC|NNP|_ mm10|mm10|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ and|and|CC|_ raw|raw|JJ|_ fragment|fragment|NN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ isolates|isolate|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_
Following|follow|VBG|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ TruSeq|truseq|NN|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|Preparation|NNP|_ Guide|Guide|NNP|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Strains|strain|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ MH|mh|NN|_ broth|broth|NN|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Human|human|JJ|_
No|no|DT|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 25922|25922|CD|_
Strains|strain|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ MH|mh|NN|_ broth|broth|NN|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Human|human|JJ|_
No|no|DT|_ treatment|treatment|NN|_
Ganlin|ganlin|NN|_ ,|,|,|_ ,|,|,|_ Xu|Xu|NNP|_
RNA-Seq|rna-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ done|do|VBN|_ using|use|VBG|_ blind|blind|JJ|_ and|and|CC|_ fit-only|fit-only|JJ|_ parameter|parameter|NN|_ in|in|IN|_ DE-Seq|de-seq|NN|_ pakage|pakage|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ FASTX-Toolkit|fastx-toolkit|NN|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ and|and|CC|_ Perl|Perl|NNP|_ version|version|NN|_ 5.8.8|5.8.8|CD|_
first|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ the|the|DT|_ use|use|NN|_ of|of|IN|_ SuperScriptII|superscriptii|NN|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ done|do|VBN|_ before|before|IN|_ end-pair|end-pair|JJ|_ and|and|CC|_ dA-tailing|da-tailing|JJ|_
Reads|read|VBZ|_ longer|longer|JJR|_ than|than|IN|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ ≤|≤|NN|_ 2|2|CD|_ N|n|NN|_ -LRB-|-lrb-|-LRB-|_ ambiguous|ambiguous|JJ|_ nucleotides|nucleotide|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ preserved|preserve|VBN|_ .|.|.|_
Using|use|VBG|_ blind|blind|JJ|_ and|and|CC|_ fit-only|fit-only|JJ|_ parameter|parameter|NN|_ in|in|IN|_ DE-Seq|de-seq|NN|_ pakage|pakage|NN|_ ,|,|,|_ expressions|expression|NNS|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ samples|sample|NNS|_ were|be|VBD|_ changed|change|VBN|_ to|to|TO|_ count|count|VB|_ per|per|IN|_ gene|gene|NN|_ ,|,|,|_ using|use|VBG|_ RNA-Seq|rna-seq|NN|_ protocol|protocol|NN|_ on|on|IN|_ Illumina|Illumina|NNP|_ HiSeq2500|HiSeq2500|NNP|_ platform|platform|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ UCSC|UCSC|NNP|_ mm10|mm10|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ and|and|CC|_ raw|raw|JJ|_ fragment|fragment|NN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ isolates|isolate|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_
Following|follow|VBG|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ TruSeq|truseq|NN|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|Preparation|NNP|_ Guide|Guide|NNP|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Strains|strain|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ MH|mh|NN|_ broth|broth|NN|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Broiler|broiler|NN|_ Fecal|fecal|JJ|_
No|no|DT|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Poultry|Poultry|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Virulent|virulent|JJ|_ and|and|CC|_ multidrug|multidrug|JJ|_ resistant|resistant|JJ|_
Strains|strain|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ MH|mh|NN|_ broth|broth|NN|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Broiler|broiler|NN|_ Fecal|fecal|JJ|_
No|no|DT|_ treatment|treatment|NN|_
Ganlin|ganlin|NN|_ ,|,|,|_ ,|,|,|_ Xu|Xu|NNP|_
RNA-Seq|rna-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ done|do|VBN|_ using|use|VBG|_ blind|blind|JJ|_ and|and|CC|_ fit-only|fit-only|JJ|_ parameter|parameter|NN|_ in|in|IN|_ DE-Seq|de-seq|NN|_ pakage|pakage|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ FASTX-Toolkit|fastx-toolkit|NN|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ and|and|CC|_ Perl|Perl|NNP|_ version|version|NN|_ 5.8.8|5.8.8|CD|_
first|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ the|the|DT|_ use|use|NN|_ of|of|IN|_ SuperScriptII|superscriptii|NN|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ done|do|VBN|_ before|before|IN|_ end-pair|end-pair|JJ|_ and|and|CC|_ dA-tailing|da-tailing|JJ|_
Reads|read|VBZ|_ longer|longer|JJR|_ than|than|IN|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ ≤|≤|NN|_ 2|2|CD|_ N|n|NN|_ -LRB-|-lrb-|-LRB-|_ ambiguous|ambiguous|JJ|_ nucleotides|nucleotide|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ preserved|preserve|VBN|_ .|.|.|_
Using|use|VBG|_ blind|blind|JJ|_ and|and|CC|_ fit-only|fit-only|JJ|_ parameter|parameter|NN|_ in|in|IN|_ DE-Seq|de-seq|NN|_ pakage|pakage|NN|_ ,|,|,|_ expressions|expression|NNS|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ samples|sample|NNS|_ were|be|VBD|_ changed|change|VBN|_ to|to|TO|_ count|count|VB|_ per|per|IN|_ gene|gene|NN|_ ,|,|,|_ using|use|VBG|_ RNA-Seq|rna-seq|NN|_ protocol|protocol|NN|_ on|on|IN|_ Illumina|Illumina|NNP|_ HiSeq2500|HiSeq2500|NNP|_ platform|platform|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ UCSC|UCSC|NNP|_ mm10|mm10|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ and|and|CC|_ raw|raw|JJ|_ fragment|fragment|NN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ isolates|isolate|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_
Following|follow|VBG|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ TruSeq|truseq|NN|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|Preparation|NNP|_ Guide|Guide|NNP|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Strains|strain|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ MH|mh|NN|_ broth|broth|NN|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Broiler|broiler|NN|_ Fecal|fecal|JJ|_
No|no|DT|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Poultry|Poultry|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Virulent|virulent|JJ|_ and|and|CC|_ multidrug|multidrug|JJ|_ resistant|resistant|JJ|_
Strains|strain|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ MH|mh|NN|_ broth|broth|NN|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Broiler|broiler|NN|_ Fecal|fecal|JJ|_
No|no|DT|_ treatment|treatment|NN|_
Ganlin|ganlin|NN|_ ,|,|,|_ ,|,|,|_ Xu|Xu|NNP|_
Illumina|Illumina|NNP|_ fastq|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ submitted|submit|VBN|_ to|to|TO|_ the|the|DT|_ galaxy|galaxy|NN|_ pipeline|pipeline|NN|_ =|=|JJ|_ >|>|JJR|_ grooming|grooming|NN|_ =|=|JJ|_ >|>|JJR|_ mapping|mapping|NN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 002655|002655|CD|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ default|default|NN|_ but|but|CC|_ seed|seed|NN|_ 19|19|CD|_ nt|nt|NNS|_ &|&|CC|_ zero|zero|CD|_ mismatches|mismatch|NNS|_ within|within|IN|_ seed|seed|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655|002655|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Reads|read|NNS|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ and|and|CC|_ RCV|RCV|NNP|_ mapped|map|VBD|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 002655|002655|CD|_ -LRB-|-lrb-|-LRB-|_ RCV|rcv|NN|_ =|=|JJ|_ Ribosomal|ribosomal|JJ|_ Coverage|Coverage|NNP|_ Value|value|NN|_ =|=|JJ|_ RPKM-footprint|rpkm-footprint|NN|_ over|over|IN|_ RPKM-transcription|rpkm-transcription|NN|_ -RRB-|-rrb-|-RRB-|_
Trizol|trizol|NN|_ for|for|IN|_ RNAseq|rnaseq|NN|_ ,|,|,|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ =|=|JJ|_ >|>|JJR|_ RNase|rnase|NN|_ digestions|digestion|NNS|_ =|=|JJ|_ >|>|JJR|_ Trizol|trizol|NN|_ =|=|JJ|_ >|>|JJR|_ gel|gel|NN|_ extraction|extraction|NN|_ for|for|IN|_ RIBOseq|riboseq|NN|_
Truseq|truseq|NN|_ Small|small|JJ|_ RNA|rna|NN|_
ligation|ligation|NN|_ ,|,|,|_ rt-PCR|rt-pcr|NN|_ ,|,|,|_ PCR|pcr|NN|_
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ ,|,|,|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ between|between|IN|_ exponential|exponential|JJ|_ and|and|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
biomass|biomass|NN|_ collected|collect|VBN|_ in|in|IN|_ the|the|DT|_ transition|transition|NN|_ between|between|IN|_ exponential|exponential|JJ|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
RNA-Seq|rna-seq|NN|_
growth|growth|NN|_ media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ ,|,|,|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ between|between|IN|_ exponential|exponential|JJ|_ and|and|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
biomass|biomass|NN|_ collected|collect|VBN|_ in|in|IN|_ the|the|DT|_ transition|transition|NN|_ between|between|IN|_ exponential|exponential|JJ|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
Klaus|Klaus|NNP|_ ,|,|,|_ ,|,|,|_ Neuhaus|Neuhaus|NNP|_
We|we|PRP|_ use|use|VBP|_ Rockhopper|Rockhopper|NNP|_ for|for|IN|_ alignment|alignment|NN|_ and|and|CC|_ the|the|DT|_ complete|complete|JJ|_ analysis|analysis|NN|_ of|of|IN|_ data|datum|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 018220|018220|CD|_ and|and|CC|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ the|the|DT|_ average|average|NN|_ of|of|IN|_ the|the|DT|_ expression|expression|NN|_ values|value|NNS|_ obtained|obtain|VBN|_ in|in|IN|_ Rockhopper|Rockhopper|NNP|_ for|for|IN|_ the|the|DT|_ replicates|replicate|VBZ|_ of|of|IN|_ each|each|DT|_ condition|condition|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ T1E|t1e|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|NN|_ of|of|IN|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ samples|sample|NNS|_ DOT-T1E|dot-t1e|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CoT1E|cot1e|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|JJ|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ reads|read|VBZ|_ related|related|JJ|_ with|with|IN|_ DOT-T1E|dot-t1e|NN|_ strain|strain|NN|_ in|in|IN|_ samples|sample|NNS|_ Co-culture|co-culture|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ K12|k12|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|NN|_ of|of|IN|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ samples|sample|NNS|_ MG1655|mg1655|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CoK12|cok12|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|JJ|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ reads|read|VBZ|_ related|related|JJ|_ with|with|IN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ in|in|IN|_ samples|sample|NNS|_ Co-culture|co-culture|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Single|single|JJ|_ colonies|colony|NNS|_ of|of|IN|_ P.|P.|NNP|_ putida|putida|NN|_ strain|strain|NN|_ DOT-T1E|dot-t1e|NN|_ and|and|CC|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ --|--|:|_ Bertani|Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.01|0.01|CD|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ medium|medium|NN|_ and|and|CC|_ 50|50|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ disposed|dispose|VBN|_ in|in|RP|_ separate|separate|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ at|at|IN|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ sub-lethal|sub-lethal|JJ|_ concentrations|concentration|NNS|_ to|to|TO|_ the|the|DT|_ culture|culture|NN|_ medium|medium|NN|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ µg/ml|µg/ml|NN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 300|300|CD|_ µg/ml|µg/ml|JJ|_ ampicillin|ampicillin|NN|_ ,|,|,|_ 150|150|CD|_ µg/ml|µg/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ ,|,|,|_ 4|4|CD|_ µg/ml|µg/ml|NN|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 0.5|0.5|CD|_ µg/ml|µg/ml|JJ|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 300|300|CD|_ µg/ml|µg/ml|NN|_ spectinomycin|spectinomycin|NN|_ ,|,|,|_ 500|500|CD|_ µg/ml|µg/ml|JJ|_ rifampicin|rifampicin|NN|SUPP and|and|CC|_ 2|2|CD|_ µg/ml|µg/ml|JJ|_ gentamicin|gentamicin|NN|_ .|.|.|_ Then|then|RB|_ cultures|culture|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ conditions|condition|NNS|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ more|more|RBR|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ g|g|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ suspended|suspend|VBN|_ immediately|immediately|RB|_ in|in|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ After|after|IN|_ that|that|DT|_ ,|,|,|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ Trizol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Removal|removal|NN|_ of|of|IN|_ DNA|dna|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ by|by|IN|_ treatment|treatment|NN|_ with|with|IN|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ combination|combination|NN|_ with|with|IN|_ the|the|DT|_ RNase|rnase|NN|_ inhibitor|inhibitor|NN|_ RiboLock|ribolock|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ and|and|CC|_ quality|quality|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ _|_|CD|_ LB|lb|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ _|_|CD|_ LB|lb|NN|_
Carlos|Carlos|NNP|_ ,|,|,|_ Molina|Molina|NNP|_ ,|,|,|_ Santiago|Santiago|NNP|_
We|we|PRP|_ use|use|VBP|_ Rockhopper|Rockhopper|NNP|_ for|for|IN|_ alignment|alignment|NN|_ and|and|CC|_ the|the|DT|_ complete|complete|JJ|_ analysis|analysis|NN|_ of|of|IN|_ data|datum|NNS|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 018220|018220|CD|_ and|and|CC|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ the|the|DT|_ average|average|NN|_ of|of|IN|_ the|the|DT|_ expression|expression|NN|_ values|value|NNS|_ obtained|obtain|VBN|_ in|in|IN|_ Rockhopper|Rockhopper|NNP|_ for|for|IN|_ the|the|DT|_ replicates|replicate|VBZ|_ of|of|IN|_ each|each|DT|_ condition|condition|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ T1E|t1e|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|NN|_ of|of|IN|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ samples|sample|NNS|_ DOT-T1E|dot-t1e|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CoT1E|cot1e|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|JJ|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ reads|read|VBZ|_ related|related|JJ|_ with|with|IN|_ DOT-T1E|dot-t1e|NN|_ strain|strain|NN|_ in|in|IN|_ samples|sample|NNS|_ Co-culture|co-culture|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ K12|k12|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|NN|_ of|of|IN|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ samples|sample|NNS|_ MG1655|mg1655|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CoK12|cok12|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|JJ|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ reads|read|VBZ|_ related|related|JJ|_ with|with|IN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ in|in|IN|_ samples|sample|NNS|_ Co-culture|co-culture|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Single|single|JJ|_ colonies|colony|NNS|_ of|of|IN|_ P.|P.|NNP|_ putida|putida|NN|_ strain|strain|NN|_ DOT-T1E|dot-t1e|NN|_ and|and|CC|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ --|--|:|_ Bertani|Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.01|0.01|CD|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ medium|medium|NN|_ and|and|CC|_ 50|50|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ disposed|dispose|VBN|_ in|in|RP|_ separate|separate|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ at|at|IN|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ sub-lethal|sub-lethal|JJ|_ concentrations|concentration|NNS|_ to|to|TO|_ the|the|DT|_ culture|culture|NN|_ medium|medium|NN|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ µg/ml|µg/ml|NN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 300|300|CD|_ µg/ml|µg/ml|JJ|_ ampicillin|ampicillin|NN|_ ,|,|,|_ 150|150|CD|_ µg/ml|µg/ml|JJ|_ chloramphenicol|chloramphenicol|NN|_ ,|,|,|_ 4|4|CD|_ µg/ml|µg/ml|NN|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 0.5|0.5|CD|_ µg/ml|µg/ml|JJ|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 300|300|CD|_ µg/ml|µg/ml|NN|_ spectinomycin|spectinomycin|NN|_ ,|,|,|_ 500|500|CD|_ µg/ml|µg/ml|JJ|_ rifampicin|rifampicin|NN|SUPP and|and|CC|_ 2|2|CD|_ µg/ml|µg/ml|JJ|_ gentamicin|gentamicin|NN|_ .|.|.|_ Then|then|RB|_ cultures|culture|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ conditions|condition|NNS|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ more|more|RBR|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ g|g|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ suspended|suspend|VBN|_ immediately|immediately|RB|_ in|in|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v/v|v/v|NN|_ -RRB-|-rrb-|-RRB-|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ After|after|IN|_ that|that|DT|_ ,|,|,|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ Trizol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Removal|removal|NN|_ of|of|IN|_ DNA|dna|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ by|by|IN|_ treatment|treatment|NN|_ with|with|IN|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ combination|combination|NN|_ with|with|IN|_ the|the|DT|_ RNase|rnase|NN|_ inhibitor|inhibitor|NN|_ RiboLock|ribolock|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ and|and|CC|_ quality|quality|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ _|_|CD|_ LB|lb|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ _|_|CD|_ LB|lb|NN|_
Carlos|Carlos|NNP|_ ,|,|,|_ Molina|Molina|NNP|_ ,|,|,|_ Santiago|Santiago|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time0|time0|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time2|time2|CD|_ .5|.5|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time5|time5|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time7|time7|CD|_ .5|.5|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time10|time10|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time20|time20|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time0|time0|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time2|time2|CD|_ .5|.5|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time7|time7|CD|_ .5|.5|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ SK4455|sk4455|NNS|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ rnc|rnc|SYM|GEN -|-|:|_ deletion|deletion|NN|_ mutant|mutant|JJ|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time0|time0|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ SK4455|sk4455|NNS|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ rnc|rnc|SYM|GEN -|-|:|_ deletion|deletion|NN|_ mutant|mutant|JJ|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time2|time2|CD|_ .5|.5|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ SK4455|sk4455|NNS|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ rnc|rnc|SYM|GEN -|-|:|_ deletion|deletion|NN|_ mutant|mutant|JJ|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time5|time5|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ SK4455|sk4455|NNS|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ rnc|rnc|SYM|GEN -|-|:|_ deletion|deletion|NN|_ mutant|mutant|JJ|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time7|time7|CD|_ .5|.5|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ SK4455|sk4455|NNS|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ rnc|rnc|SYM|GEN -|-|:|_ deletion|deletion|NN|_ mutant|mutant|JJ|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time10|time10|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
Adapters|Adapters|NNPS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ SK4455|sk4455|NNS|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ rnc|rnc|SYM|GEN -|-|:|_ deletion|deletion|NN|_ mutant|mutant|JJ|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time20|time20|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg/ml|μg/ml|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stop|stop|VB|_ nascent|nascent|JJ|_ transcription|transcription|NN|_ and|and|CC|_ quenched|quench|VBN|_ with|with|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ timepoint|timepoint|NN|_ was|be|VBD|_ taken|take|VBN|_ 3.5|3.5|CD|_ minutes|minute|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ give|give|VB|_ time|time|NN|_ for|for|IN|_ the|the|DT|_ diffusion|diffusion|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP into|into|IN|_ the|the|DT|_ cells|cell|NNS|_ and|and|CC|_ binding|binding|NN|_ of|of|IN|_ the|the|DT|_ antibiotic|antibiotic|JJ|_ to|to|TO|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ This|this|DT|_ sample|sample|NN|_ was|be|VBD|_ called|call|VBN|_ 0|0|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ further|further|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ 2.5|2.5|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 7.5|7.5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ from|from|IN|_ wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ the|the|DT|_ RNase|rnase|NN|_ III|iii|CD|_ mutant|mutant|NN|_ .|.|.|_ A|a|DT|_ partial|partial|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ wild-type|wild-type|JJ|_ was|be|VBD|_ taken|take|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ ,|,|,|_ 2.5|2.5|CD|_ ,|,|,|_ and|and|CC|_ 7.5|7.5|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ reproducibility|reproducibility|NN|_ between|between|IN|_ samples|sample|NNS|_ .|.|.|_
Gina|Gina|NNP|_ ,|,|,|_ ,|,|,|_ Gordon|Gordon|NNP|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_
FastQ|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ examined|examine|VBN|_ using|use|VBG|_ the|the|DT|_ FastQC|fastqc|NN|_ tool|tool|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ from|from|IN|_ 3|3|CD|_ '|'|''|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ Cutadapt|cutadapt|JJ|_ v1|v1|NN|_ .10|.10|CD|_ ,|,|,|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 15|15|CD|_ nucleotides|nucleotide|NNS|_ .|.|.|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v1|v1|NN|_ .1.2|.1.2|CD|_ ,|,|,|_ by|by|IN|_ allowing|allow|VBG|_ up|up|RP|_ to|to|TO|_ 7|7|CD|_ mapping|mapping|NN|_ positions|position|NNS|_ to|to|TO|_ enable|enable|VB|_ mapping|map|VBG|_ to|to|TO|_ the|the|DT|_ 7|7|CD|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ parameters|parameter|NNS|_ :|:|:|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -|-|:|_ m|m|NN|_ 7|7|CD|_ -|-|:|_ a|a|DT|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ -5|-5|CD|_ 5|5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ rescaled|rescale|VBN|_ to|to|TO|_ a|a|DT|_ size|size|NN|_ of|of|IN|_ 10|10|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ BEDGraph|bedgraph|NN|_ files|file|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ genomeCoverageBed|genomecoveragebed|JJ|_ utility|utility|NN|_ of|of|IN|_ the|the|DT|_ BEDTools|bedtool|NNS|_ suite|suite|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ DMS-seq|dms-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pooled|JJ|_ Total|total|JJ|_ and|and|CC|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pooled|JJ|_ Total|total|JJ|_ and|and|CC|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ from|from|IN|_ both|both|DT|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ analyzed|analyze|VBN|_ transcript|transcript|NN|_ ,|,|,|_ 10|10|CD|_ files|file|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ SPET-seq|spet-seq|JJ|_ data|datum|NNS|_ for|for|IN|_ the|the|DT|_ 10|10|CD|_ transcription|transcription|NN|_ deciles|decile|NNS|_ are|be|VBP|_ provided|provide|VBN|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ A|a|DT|_ file|file|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ each|each|DT|_ transcription|transcription|NN|_ intermediate|intermediate|NN|_ is|be|VBZ|_ provided|provide|VBN|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Each|each|DT|_ bacteria|bacterium|NNS|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ 25|25|CD|_ ml|ml|NN|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ homogeneously|homogeneously|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200|200|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|Buffer|NNP|_ A|A|NNP|_ -LSB-|-lsb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ Sucrose|sucrose|NN|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 50|50|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|buffer|NN|_ B|b|NN|_ -LSB-|-lsb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ;|;|:|_ 120|120|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ µl|µl|NN|_ Ready-Lyse|ready-lyse|NN|_ ™|™|CD|_ Lysozyme|Lysozyme|NNP|_ Solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ R1810M|r1810m|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ dropwise|dropwise|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ vial|vial|NN|_ was|be|VBD|_ gently|gently|RB|_ tilted|tilted|JJ|_ 5|5|CD|_ times|time|NNS|_ to|to|TO|_ ensure|ensure|VB|_ homogenous|homogenous|JJ|_ mixing|mix|VBG|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ 250|250|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|buffer|NN|_ C|c|NN|_ -LSB-|-lsb-|-LRB-|_ 0.5|0.5|CD|_ %|%|NN|_ Tween-20|tween-20|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ NaDOC|nadoc|NN|_ ;|;|:|_ 2|2|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ;|;|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ dropwise|dropwise|NN|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ At|at|IN|_ this|this|DT|_ stage|stage|NN|_ the|the|DT|_ solution|solution|NN|_ clears|clear|VBZ|_ considerably|considerably|RB|_ without|without|IN|_ increasing|increase|VBG|_ its|its|PRP$|_ viscosity|viscosity|NN|_ ,|,|,|_ and|and|CC|_ nucleoid|nucleoid|JJ|_ becomes|become|VBZ|_ visible|visible|JJ|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ cut|cut|NN|_ P1000|p1000|NN|_ pipette|pipette|NN|_ tip|tip|NN|_ ,|,|,|_ the|the|DT|_ whole|whole|JJ|_ sample|sample|NN|_ was|be|VBD|_ gently|gently|RB|_ layered|layer|VBN|_ on|on|IN|_ the|the|DT|_ top|top|NN|_ of|of|IN|_ a|a|DT|_ 5-30|5-30|CD|_ %|%|NN|_ w/v|w/v|NN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ -LSB-|-lsb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ 1|1|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP DTT|dtt|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 17,000|17,000|CD|_ RPM|rpm|NN|_ in|in|IN|_ a|a|DT|_ SW55Ti|sw55ti|NN|_ rotor|rotor|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 342194|342194|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 9|9|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ the|the|DT|_ nucleoid|nucleoid|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ syringe|syringe|NN|_ with|with|IN|_ a|a|DT|_ 18G|18g|NN|_ blunt|blunt|JJ|_ fill|fill|NN|_ needle|needle|NN|_ ,|,|,|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ new|new|JJ|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ .|.|.|_ The|the|DT|_ remaining|remain|VBG|_ gradient|gradient|NN|_ was|be|VBD|_ assumed|assume|VBN|_ to|to|TO|_ represent|represent|VB|_ the|the|DT|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ .|.|.|_ The|the|DT|_ nucleoid|nucleoid|NN|_ was|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 40|40|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 7.5|7.5|CD|_ ;|;|:|_ 150|150|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ;|;|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP DTT|dtt|NN|_ ;|;|:|_ 0.01|0.01|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ pulse|pulse|NN|_ vortexed|vortex|VBD|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 28,000|28,000|CD|_ RPM|rpm|NN|_ in|in|IN|_ a|a|DT|_ SW55Ti|sw55ti|NN|_ rotor|rotor|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ nucleoid|nucleoid|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ 2|2|CD|_ ml|ml|NN|_ of|of|IN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ ,|,|,|_ taking|take|VBG|_ care|care|NN|_ not|not|RB|_ to|to|TO|_ disturb|disturb|VB|_ it|it|PRP|_ .|.|.|_ The|the|DT|_ nucleoid|nucleoid|NN|_ was|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ µl|µl|NN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ ,|,|,|_ and|and|CC|_ solubilized|solubilize|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 0.1|0.1|CD|_ gr|gr|NN|_ acid-washed|acid-washed|JJ|_ glass|glass|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ G1145|g1145|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ shaking|shake|VBG|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ in|in|IN|_ a|a|DT|_ TissueLyser|TissueLyser|NNP|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ each|each|DT|_ 100|100|CD|_ µl|µl|NN|_ of|of|IN|_ purified|purify|VBN|_ nucleoids|nucleoid|NNS|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TRIzol|trizol|NN|_ ®|®|CD|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 15596-018|15596-018|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ all|all|DT|_ experiments|experiment|NNS|_ ,|,|,|_ RNA|rna|NN|_ from|from|IN|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -LRB-|-lrb-|-LRB-|_ corresponding|correspond|VBG|_ to|to|TO|_ mature|mature|JJ|_ RNA|rna|NN|_ species|species|NNS|_ -RRB-|-rrb-|-RRB-|_ had|have|VBD|_ RIN|RIN|NNP|_ >|>|JJR|_ 9.5|9.5|CD|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ yield|yield|NN|_ from|from|IN|_ nucleoid|nucleoid|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ ~|~|CD|_ 6|6|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ content|content|NN|_ .|.|.|_
10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ pre-adenylated|pre-adenylated|JJ|_ -LRB-|-lrb-|-LRB-|_ rApp|rapp|NN|_ -RRB-|-rrb-|-RRB-|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ nascent|nascent|JJ|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ mature|mature|JJ|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ in|in|IN|_ a|a|DT|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 20|20|CD|_ μl|μl|NN|_ ,|,|,|_ using|use|VBG|_ 400|400|CD|_ U|U|NNP|_ T4|t4|NN|_ RNA|rna|NN|_ Ligase|ligase|NN|_ 2|2|CD|_ ,|,|,|_ Deletion|deletion|NN|_ Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ LR2D11310K|lr2d11310k|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20|20|CD|_ %|%|NN|_ PEG-8000|peg-8000|NN|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ Fragmentation|fragmentation|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 65|65|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.3|8.3|CD|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ;|;|:|_ 5|5|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragment|VBN|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ in|in|IN|_ 5.5|5.5|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ heat-denatured|heat-denatured|JJ|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ volume|volume|NN|_ of|of|IN|_ 10|10|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP dNTPs|dntp|NNS|_ ,|,|,|_ 5|5|CD|_ pmol|pmol|NN|_ of|of|IN|_ RT|rt|NN|_ primer|primer|NN|_ ,|,|,|_ 20|20|CD|_ U|U|NNP|_ RNaseOUT|RNaseOUT|NNP|_ ™|™|NNP|_ Recombinant|recombinant|JJ|_ Ribonuclease|ribonuclease|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 10777-019|10777-019|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ SuperScript|SuperScript|NNP|_ ®|®|SYM|_ III|iii|CD|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 18080-044|18080-044|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 50|50|CD|_ °C|°c|NN|_ for|for|IN|_ 50|50|CD|_ minutes|minute|NNS|_ .|.|.|_ Template|template|NN|_ RNA|rna|NN|_ was|be|VBD|_ degraded|degrade|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ μl|μl|NN|_ of|of|IN|_ 1|1|CD|_ M|m|NN|_ NaOH|naoh|NN|_ ,|,|,|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 6|6|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ resolved|resolve|VBN|_ on|on|IN|_ a|a|DT|_ 10|10|CD|_ %|%|NN|_ TBE-Urea|tbe-urea|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ gel|gel|NN|_ slice|slice|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ fragments|fragment|NNS|_ in|in|IN|_ the|the|DT|_ range|range|NN|_ 40-150|40-150|CD|_ nt|nt|NN|_ was|be|VBD|_ cut|cut|VBN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ passive|passive|NN|_ diffusion|diffusion|NN|_ in|in|IN|_ Diffusion|Diffusion|NNP|_ buffer|buffer|NN|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ moderate|moderate|JJ|_ shaking|shake|VBG|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ ml|ml|NN|_ Isopropanol|isopropanol|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ μl|μl|NN|_ Glycogen|glycogen|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ μg/μl|μg/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 8.25|8.25|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ 10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ phosphorylated|phosphorylate|VBN|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ -|-|:|_ OH|oh|NN|_ of|of|IN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.05|0.05|CD|_ mM|mm|NN|KWSUPP ATP|atp|NN|SUPP ,|,|,|_ 20|20|CD|_ %|%|NN|_ PEG-4000|peg-4000|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ CircLigase|CircLigase|NNP|_ ™|™|NNP|_ II|II|NNP|_ ssDNA|ssDNA|NNP|_ Ligase|Ligase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ CL9025K|cl9025k|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 60|60|CD|_ °C|°c|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ ,|,|,|_ and|and|CC|_ 68|68|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ excess|excess|JJ|_ adapter|adapter|NN|_ using|use|VBG|_ 1.8|1.8|CD|_ volumes|volume|NNS|_ of|of|IN|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ A63881|a63881|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ ,|,|,|_ and|and|CC|_ indexed|index|VBD|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ introduced|introduce|VBN|_ by|by|IN|_ 15|15|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 25|25|CD|_ pmol|pmol|NN|_ of|of|IN|_ each|each|DT|_ primer|primer|NN|_ ,|,|,|_ and|and|CC|_ 25|25|CD|_ μl|μl|NN|_ NEBNext|nebnext|NN|_ ®|®|CD|_ High-Fidelity|high-fidelity|NN|_ 2X|2x|NN|_ PCR|pcr|NN|_ Master|master|NN|_ Mix|Mix|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ M0541L|m0541l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
substr|substr|NN|_ :|:|:|_ MG1655|mg1655|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ Cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_
Danny|Danny|NNP|_ ,|,|,|_ ,|,|,|_ Incarnato|Incarnato|NNP|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_
FastQ|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ examined|examine|VBN|_ using|use|VBG|_ the|the|DT|_ FastQC|fastqc|NN|_ tool|tool|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ from|from|IN|_ 3|3|CD|_ '|'|''|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ Cutadapt|cutadapt|JJ|_ v1|v1|NN|_ .10|.10|CD|_ ,|,|,|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 15|15|CD|_ nucleotides|nucleotide|NNS|_ .|.|.|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v1|v1|NN|_ .1.2|.1.2|CD|_ ,|,|,|_ by|by|IN|_ allowing|allow|VBG|_ up|up|RP|_ to|to|TO|_ 7|7|CD|_ mapping|mapping|NN|_ positions|position|NNS|_ to|to|TO|_ enable|enable|VB|_ mapping|map|VBG|_ to|to|TO|_ the|the|DT|_ 7|7|CD|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ parameters|parameter|NNS|_ :|:|:|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -|-|:|_ m|m|NN|_ 7|7|CD|_ -|-|:|_ a|a|DT|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ -5|-5|CD|_ 5|5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ rescaled|rescale|VBN|_ to|to|TO|_ a|a|DT|_ size|size|NN|_ of|of|IN|_ 10|10|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ BEDGraph|bedgraph|NN|_ files|file|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ genomeCoverageBed|genomecoveragebed|JJ|_ utility|utility|NN|_ of|of|IN|_ the|the|DT|_ BEDTools|bedtool|NNS|_ suite|suite|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ DMS-seq|dms-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pooled|JJ|_ Total|total|JJ|_ and|and|CC|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pooled|JJ|_ Total|total|JJ|_ and|and|CC|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ from|from|IN|_ both|both|DT|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ analyzed|analyze|VBN|_ transcript|transcript|NN|_ ,|,|,|_ 10|10|CD|_ files|file|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ SPET-seq|spet-seq|JJ|_ data|datum|NNS|_ for|for|IN|_ the|the|DT|_ 10|10|CD|_ transcription|transcription|NN|_ deciles|decile|NNS|_ are|be|VBP|_ provided|provide|VBN|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ A|a|DT|_ file|file|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ each|each|DT|_ transcription|transcription|NN|_ intermediate|intermediate|NN|_ is|be|VBZ|_ provided|provide|VBN|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Each|each|DT|_ bacteria|bacterium|NNS|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ 25|25|CD|_ ml|ml|NN|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ homogeneously|homogeneously|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200|200|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|Buffer|NNP|_ A|A|NNP|_ -LSB-|-lsb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ Sucrose|sucrose|NN|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 50|50|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|buffer|NN|_ B|b|NN|_ -LSB-|-lsb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ;|;|:|_ 120|120|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ µl|µl|NN|_ Ready-Lyse|ready-lyse|NN|_ ™|™|CD|_ Lysozyme|Lysozyme|NNP|_ Solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ R1810M|r1810m|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ dropwise|dropwise|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ vial|vial|NN|_ was|be|VBD|_ gently|gently|RB|_ tilted|tilted|JJ|_ 5|5|CD|_ times|time|NNS|_ to|to|TO|_ ensure|ensure|VB|_ homogenous|homogenous|JJ|_ mixing|mix|VBG|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ 250|250|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|buffer|NN|_ C|c|NN|_ -LSB-|-lsb-|-LRB-|_ 0.5|0.5|CD|_ %|%|NN|_ Tween-20|tween-20|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ NaDOC|nadoc|NN|_ ;|;|:|_ 2|2|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ;|;|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ dropwise|dropwise|NN|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ At|at|IN|_ this|this|DT|_ stage|stage|NN|_ the|the|DT|_ solution|solution|NN|_ clears|clear|VBZ|_ considerably|considerably|RB|_ without|without|IN|_ increasing|increase|VBG|_ its|its|PRP$|_ viscosity|viscosity|NN|_ ,|,|,|_ and|and|CC|_ nucleoid|nucleoid|JJ|_ becomes|become|VBZ|_ visible|visible|JJ|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ cut|cut|NN|_ P1000|p1000|NN|_ pipette|pipette|NN|_ tip|tip|NN|_ ,|,|,|_ the|the|DT|_ whole|whole|JJ|_ sample|sample|NN|_ was|be|VBD|_ gently|gently|RB|_ layered|layer|VBN|_ on|on|IN|_ the|the|DT|_ top|top|NN|_ of|of|IN|_ a|a|DT|_ 5-30|5-30|CD|_ %|%|NN|_ w/v|w/v|NN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ -LSB-|-lsb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ 1|1|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP DTT|dtt|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 17,000|17,000|CD|_ RPM|rpm|NN|_ in|in|IN|_ a|a|DT|_ SW55Ti|sw55ti|NN|_ rotor|rotor|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 342194|342194|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 9|9|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ the|the|DT|_ nucleoid|nucleoid|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ syringe|syringe|NN|_ with|with|IN|_ a|a|DT|_ 18G|18g|NN|_ blunt|blunt|JJ|_ fill|fill|NN|_ needle|needle|NN|_ ,|,|,|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ new|new|JJ|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ .|.|.|_ The|the|DT|_ remaining|remain|VBG|_ gradient|gradient|NN|_ was|be|VBD|_ assumed|assume|VBN|_ to|to|TO|_ represent|represent|VB|_ the|the|DT|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ .|.|.|_ The|the|DT|_ nucleoid|nucleoid|NN|_ was|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 40|40|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 7.5|7.5|CD|_ ;|;|:|_ 150|150|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ;|;|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP DTT|dtt|NN|_ ;|;|:|_ 0.01|0.01|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ pulse|pulse|NN|_ vortexed|vortex|VBD|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 28,000|28,000|CD|_ RPM|rpm|NN|_ in|in|IN|_ a|a|DT|_ SW55Ti|sw55ti|NN|_ rotor|rotor|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ nucleoid|nucleoid|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ 2|2|CD|_ ml|ml|NN|_ of|of|IN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ ,|,|,|_ taking|take|VBG|_ care|care|NN|_ not|not|RB|_ to|to|TO|_ disturb|disturb|VB|_ it|it|PRP|_ .|.|.|_ The|the|DT|_ nucleoid|nucleoid|NN|_ was|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ µl|µl|NN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ ,|,|,|_ and|and|CC|_ solubilized|solubilize|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 0.1|0.1|CD|_ gr|gr|NN|_ acid-washed|acid-washed|JJ|_ glass|glass|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ G1145|g1145|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ shaking|shake|VBG|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ in|in|IN|_ a|a|DT|_ TissueLyser|TissueLyser|NNP|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ each|each|DT|_ 100|100|CD|_ µl|µl|NN|_ of|of|IN|_ purified|purify|VBN|_ nucleoids|nucleoid|NNS|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TRIzol|trizol|NN|_ ®|®|CD|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 15596-018|15596-018|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ all|all|DT|_ experiments|experiment|NNS|_ ,|,|,|_ RNA|rna|NN|_ from|from|IN|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -LRB-|-lrb-|-LRB-|_ corresponding|correspond|VBG|_ to|to|TO|_ mature|mature|JJ|_ RNA|rna|NN|_ species|species|NNS|_ -RRB-|-rrb-|-RRB-|_ had|have|VBD|_ RIN|RIN|NNP|_ >|>|JJR|_ 9.5|9.5|CD|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ yield|yield|NN|_ from|from|IN|_ nucleoid|nucleoid|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ ~|~|CD|_ 6|6|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ content|content|NN|_ .|.|.|_
10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ pre-adenylated|pre-adenylated|JJ|_ -LRB-|-lrb-|-LRB-|_ rApp|rapp|NN|_ -RRB-|-rrb-|-RRB-|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ nascent|nascent|JJ|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ mature|mature|JJ|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ in|in|IN|_ a|a|DT|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 20|20|CD|_ μl|μl|NN|_ ,|,|,|_ using|use|VBG|_ 400|400|CD|_ U|U|NNP|_ T4|t4|NN|_ RNA|rna|NN|_ Ligase|ligase|NN|_ 2|2|CD|_ ,|,|,|_ Deletion|deletion|NN|_ Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ LR2D11310K|lr2d11310k|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20|20|CD|_ %|%|NN|_ PEG-8000|peg-8000|NN|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ Fragmentation|fragmentation|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 65|65|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.3|8.3|CD|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ;|;|:|_ 5|5|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragment|VBN|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ in|in|IN|_ 5.5|5.5|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ heat-denatured|heat-denatured|JJ|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ volume|volume|NN|_ of|of|IN|_ 10|10|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP dNTPs|dntp|NNS|_ ,|,|,|_ 5|5|CD|_ pmol|pmol|NN|_ of|of|IN|_ RT|rt|NN|_ primer|primer|NN|_ ,|,|,|_ 20|20|CD|_ U|U|NNP|_ RNaseOUT|RNaseOUT|NNP|_ ™|™|NNP|_ Recombinant|recombinant|JJ|_ Ribonuclease|ribonuclease|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 10777-019|10777-019|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ SuperScript|SuperScript|NNP|_ ®|®|SYM|_ III|iii|CD|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 18080-044|18080-044|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 50|50|CD|_ °C|°c|NN|_ for|for|IN|_ 50|50|CD|_ minutes|minute|NNS|_ .|.|.|_ Template|template|NN|_ RNA|rna|NN|_ was|be|VBD|_ degraded|degrade|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ μl|μl|NN|_ of|of|IN|_ 1|1|CD|_ M|m|NN|_ NaOH|naoh|NN|_ ,|,|,|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 6|6|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ resolved|resolve|VBN|_ on|on|IN|_ a|a|DT|_ 10|10|CD|_ %|%|NN|_ TBE-Urea|tbe-urea|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ gel|gel|NN|_ slice|slice|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ fragments|fragment|NNS|_ in|in|IN|_ the|the|DT|_ range|range|NN|_ 40-150|40-150|CD|_ nt|nt|NN|_ was|be|VBD|_ cut|cut|VBN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ passive|passive|NN|_ diffusion|diffusion|NN|_ in|in|IN|_ Diffusion|Diffusion|NNP|_ buffer|buffer|NN|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ moderate|moderate|JJ|_ shaking|shake|VBG|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ ml|ml|NN|_ Isopropanol|isopropanol|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ μl|μl|NN|_ Glycogen|glycogen|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ μg/μl|μg/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 8.25|8.25|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ 10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ phosphorylated|phosphorylate|VBN|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ -|-|:|_ OH|oh|NN|_ of|of|IN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.05|0.05|CD|_ mM|mm|NN|KWSUPP ATP|atp|NN|SUPP ,|,|,|_ 20|20|CD|_ %|%|NN|_ PEG-4000|peg-4000|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ CircLigase|CircLigase|NNP|_ ™|™|NNP|_ II|II|NNP|_ ssDNA|ssDNA|NNP|_ Ligase|Ligase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ CL9025K|cl9025k|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 60|60|CD|_ °C|°c|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ ,|,|,|_ and|and|CC|_ 68|68|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ excess|excess|JJ|_ adapter|adapter|NN|_ using|use|VBG|_ 1.8|1.8|CD|_ volumes|volume|NNS|_ of|of|IN|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ A63881|a63881|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ ,|,|,|_ and|and|CC|_ indexed|index|VBD|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ introduced|introduce|VBN|_ by|by|IN|_ 15|15|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 25|25|CD|_ pmol|pmol|NN|_ of|of|IN|_ each|each|DT|_ primer|primer|NN|_ ,|,|,|_ and|and|CC|_ 25|25|CD|_ μl|μl|NN|_ NEBNext|nebnext|NN|_ ®|®|CD|_ High-Fidelity|high-fidelity|NN|_ 2X|2x|NN|_ PCR|pcr|NN|_ Master|master|NN|_ Mix|Mix|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ M0541L|m0541l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
substr|substr|NN|_ :|:|:|_ MG1655|mg1655|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ Cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_
Danny|Danny|NNP|_ ,|,|,|_ ,|,|,|_ Incarnato|Incarnato|NNP|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_
FastQ|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ examined|examine|VBN|_ using|use|VBG|_ the|the|DT|_ FastQC|fastqc|NN|_ tool|tool|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ from|from|IN|_ 3|3|CD|_ '|'|''|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ Cutadapt|cutadapt|JJ|_ v1|v1|NN|_ .10|.10|CD|_ ,|,|,|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 15|15|CD|_ nucleotides|nucleotide|NNS|_ .|.|.|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v1|v1|NN|_ .1.2|.1.2|CD|_ ,|,|,|_ by|by|IN|_ allowing|allow|VBG|_ up|up|RP|_ to|to|TO|_ 7|7|CD|_ mapping|mapping|NN|_ positions|position|NNS|_ to|to|TO|_ enable|enable|VB|_ mapping|map|VBG|_ to|to|TO|_ the|the|DT|_ 7|7|CD|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ parameters|parameter|NNS|_ :|:|:|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -|-|:|_ m|m|NN|_ 7|7|CD|_ -|-|:|_ a|a|DT|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ -5|-5|CD|_ 5|5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ rescaled|rescale|VBN|_ to|to|TO|_ a|a|DT|_ size|size|NN|_ of|of|IN|_ 10|10|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ BEDGraph|bedgraph|NN|_ files|file|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ genomeCoverageBed|genomecoveragebed|JJ|_ utility|utility|NN|_ of|of|IN|_ the|the|DT|_ BEDTools|bedtool|NNS|_ suite|suite|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ DMS-seq|dms-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pooled|JJ|_ Total|total|JJ|_ and|and|CC|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pooled|JJ|_ Total|total|JJ|_ and|and|CC|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ from|from|IN|_ both|both|DT|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ analyzed|analyze|VBN|_ transcript|transcript|NN|_ ,|,|,|_ 10|10|CD|_ files|file|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ SPET-seq|spet-seq|JJ|_ data|datum|NNS|_ for|for|IN|_ the|the|DT|_ 10|10|CD|_ transcription|transcription|NN|_ deciles|decile|NNS|_ are|be|VBP|_ provided|provide|VBN|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ A|a|DT|_ file|file|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ each|each|DT|_ transcription|transcription|NN|_ intermediate|intermediate|NN|_ is|be|VBZ|_ provided|provide|VBN|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Each|each|DT|_ bacteria|bacterium|NNS|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ 25|25|CD|_ ml|ml|NN|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ homogeneously|homogeneously|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200|200|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|Buffer|NNP|_ A|A|NNP|_ -LSB-|-lsb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ Sucrose|sucrose|NN|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 50|50|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|buffer|NN|_ B|b|NN|_ -LSB-|-lsb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ;|;|:|_ 120|120|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ µl|µl|NN|_ Ready-Lyse|ready-lyse|NN|_ ™|™|CD|_ Lysozyme|Lysozyme|NNP|_ Solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ R1810M|r1810m|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ dropwise|dropwise|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ vial|vial|NN|_ was|be|VBD|_ gently|gently|RB|_ tilted|tilted|JJ|_ 5|5|CD|_ times|time|NNS|_ to|to|TO|_ ensure|ensure|VB|_ homogenous|homogenous|JJ|_ mixing|mix|VBG|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ 250|250|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|buffer|NN|_ C|c|NN|_ -LSB-|-lsb-|-LRB-|_ 0.5|0.5|CD|_ %|%|NN|_ Tween-20|tween-20|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ NaDOC|nadoc|NN|_ ;|;|:|_ 2|2|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ;|;|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ dropwise|dropwise|NN|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ At|at|IN|_ this|this|DT|_ stage|stage|NN|_ the|the|DT|_ solution|solution|NN|_ clears|clear|VBZ|_ considerably|considerably|RB|_ without|without|IN|_ increasing|increase|VBG|_ its|its|PRP$|_ viscosity|viscosity|NN|_ ,|,|,|_ and|and|CC|_ nucleoid|nucleoid|JJ|_ becomes|become|VBZ|_ visible|visible|JJ|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ cut|cut|NN|_ P1000|p1000|NN|_ pipette|pipette|NN|_ tip|tip|NN|_ ,|,|,|_ the|the|DT|_ whole|whole|JJ|_ sample|sample|NN|_ was|be|VBD|_ gently|gently|RB|_ layered|layer|VBN|_ on|on|IN|_ the|the|DT|_ top|top|NN|_ of|of|IN|_ a|a|DT|_ 5-30|5-30|CD|_ %|%|NN|_ w/v|w/v|NN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ -LSB-|-lsb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ 1|1|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP DTT|dtt|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 17,000|17,000|CD|_ RPM|rpm|NN|_ in|in|IN|_ a|a|DT|_ SW55Ti|sw55ti|NN|_ rotor|rotor|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 342194|342194|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 9|9|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ the|the|DT|_ nucleoid|nucleoid|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ syringe|syringe|NN|_ with|with|IN|_ a|a|DT|_ 18G|18g|NN|_ blunt|blunt|JJ|_ fill|fill|NN|_ needle|needle|NN|_ ,|,|,|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ new|new|JJ|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ .|.|.|_ The|the|DT|_ remaining|remain|VBG|_ gradient|gradient|NN|_ was|be|VBD|_ assumed|assume|VBN|_ to|to|TO|_ represent|represent|VB|_ the|the|DT|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ .|.|.|_ The|the|DT|_ nucleoid|nucleoid|NN|_ was|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 40|40|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 7.5|7.5|CD|_ ;|;|:|_ 150|150|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ;|;|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP DTT|dtt|NN|_ ;|;|:|_ 0.01|0.01|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ pulse|pulse|NN|_ vortexed|vortex|VBD|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 28,000|28,000|CD|_ RPM|rpm|NN|_ in|in|IN|_ a|a|DT|_ SW55Ti|sw55ti|NN|_ rotor|rotor|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ nucleoid|nucleoid|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ 2|2|CD|_ ml|ml|NN|_ of|of|IN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ ,|,|,|_ taking|take|VBG|_ care|care|NN|_ not|not|RB|_ to|to|TO|_ disturb|disturb|VB|_ it|it|PRP|_ .|.|.|_ The|the|DT|_ nucleoid|nucleoid|NN|_ was|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ µl|µl|NN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ ,|,|,|_ and|and|CC|_ solubilized|solubilize|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 0.1|0.1|CD|_ gr|gr|NN|_ acid-washed|acid-washed|JJ|_ glass|glass|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ G1145|g1145|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ shaking|shake|VBG|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ in|in|IN|_ a|a|DT|_ TissueLyser|TissueLyser|NNP|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ each|each|DT|_ 100|100|CD|_ µl|µl|NN|_ of|of|IN|_ purified|purify|VBN|_ nucleoids|nucleoid|NNS|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TRIzol|trizol|NN|_ ®|®|CD|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 15596-018|15596-018|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ all|all|DT|_ experiments|experiment|NNS|_ ,|,|,|_ RNA|rna|NN|_ from|from|IN|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -LRB-|-lrb-|-LRB-|_ corresponding|correspond|VBG|_ to|to|TO|_ mature|mature|JJ|_ RNA|rna|NN|_ species|species|NNS|_ -RRB-|-rrb-|-RRB-|_ had|have|VBD|_ RIN|RIN|NNP|_ >|>|JJR|_ 9.5|9.5|CD|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ yield|yield|NN|_ from|from|IN|_ nucleoid|nucleoid|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ ~|~|CD|_ 6|6|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ content|content|NN|_ .|.|.|_
10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ pre-adenylated|pre-adenylated|JJ|_ -LRB-|-lrb-|-LRB-|_ rApp|rapp|NN|_ -RRB-|-rrb-|-RRB-|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ nascent|nascent|JJ|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ mature|mature|JJ|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ in|in|IN|_ a|a|DT|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 20|20|CD|_ μl|μl|NN|_ ,|,|,|_ using|use|VBG|_ 400|400|CD|_ U|U|NNP|_ T4|t4|NN|_ RNA|rna|NN|_ Ligase|ligase|NN|_ 2|2|CD|_ ,|,|,|_ Deletion|deletion|NN|_ Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ LR2D11310K|lr2d11310k|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20|20|CD|_ %|%|NN|_ PEG-8000|peg-8000|NN|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ Fragmentation|fragmentation|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 65|65|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.3|8.3|CD|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ;|;|:|_ 5|5|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragment|VBN|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ in|in|IN|_ 5.5|5.5|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ heat-denatured|heat-denatured|JJ|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ volume|volume|NN|_ of|of|IN|_ 10|10|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP dNTPs|dntp|NNS|_ ,|,|,|_ 5|5|CD|_ pmol|pmol|NN|_ of|of|IN|_ RT|rt|NN|_ primer|primer|NN|_ ,|,|,|_ 20|20|CD|_ U|U|NNP|_ RNaseOUT|RNaseOUT|NNP|_ ™|™|NNP|_ Recombinant|recombinant|JJ|_ Ribonuclease|ribonuclease|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 10777-019|10777-019|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ SuperScript|SuperScript|NNP|_ ®|®|SYM|_ III|iii|CD|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 18080-044|18080-044|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 50|50|CD|_ °C|°c|NN|_ for|for|IN|_ 50|50|CD|_ minutes|minute|NNS|_ .|.|.|_ Template|template|NN|_ RNA|rna|NN|_ was|be|VBD|_ degraded|degrade|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ μl|μl|NN|_ of|of|IN|_ 1|1|CD|_ M|m|NN|_ NaOH|naoh|NN|_ ,|,|,|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 6|6|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ resolved|resolve|VBN|_ on|on|IN|_ a|a|DT|_ 10|10|CD|_ %|%|NN|_ TBE-Urea|tbe-urea|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ gel|gel|NN|_ slice|slice|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ fragments|fragment|NNS|_ in|in|IN|_ the|the|DT|_ range|range|NN|_ 40-150|40-150|CD|_ nt|nt|NN|_ was|be|VBD|_ cut|cut|VBN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ passive|passive|NN|_ diffusion|diffusion|NN|_ in|in|IN|_ Diffusion|Diffusion|NNP|_ buffer|buffer|NN|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ moderate|moderate|JJ|_ shaking|shake|VBG|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ ml|ml|NN|_ Isopropanol|isopropanol|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ μl|μl|NN|_ Glycogen|glycogen|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ μg/μl|μg/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 8.25|8.25|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ 10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ phosphorylated|phosphorylate|VBN|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ -|-|:|_ OH|oh|NN|_ of|of|IN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.05|0.05|CD|_ mM|mm|NN|KWSUPP ATP|atp|NN|SUPP ,|,|,|_ 20|20|CD|_ %|%|NN|_ PEG-4000|peg-4000|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ CircLigase|CircLigase|NNP|_ ™|™|NNP|_ II|II|NNP|_ ssDNA|ssDNA|NNP|_ Ligase|Ligase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ CL9025K|cl9025k|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 60|60|CD|_ °C|°c|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ ,|,|,|_ and|and|CC|_ 68|68|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ excess|excess|JJ|_ adapter|adapter|NN|_ using|use|VBG|_ 1.8|1.8|CD|_ volumes|volume|NNS|_ of|of|IN|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ A63881|a63881|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ ,|,|,|_ and|and|CC|_ indexed|index|VBD|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ introduced|introduce|VBN|_ by|by|IN|_ 15|15|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 25|25|CD|_ pmol|pmol|NN|_ of|of|IN|_ each|each|DT|_ primer|primer|NN|_ ,|,|,|_ and|and|CC|_ 25|25|CD|_ μl|μl|NN|_ NEBNext|nebnext|NN|_ ®|®|CD|_ High-Fidelity|high-fidelity|NN|_ 2X|2x|NN|_ PCR|pcr|NN|_ Master|master|NN|_ Mix|Mix|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ M0541L|m0541l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Nucleoid|nucleoid|NN|_ fraction|fraction|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
substr|substr|NN|_ :|:|:|_ MG1655|mg1655|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ Nucleoid|nucleoid|NN|_ fraction|fraction|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Nucleoid|nucleoid|NN|_ fraction|fraction|NN|_
Danny|Danny|NNP|_ ,|,|,|_ ,|,|,|_ Incarnato|Incarnato|NNP|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_
FastQ|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ examined|examine|VBN|_ using|use|VBG|_ the|the|DT|_ FastQC|fastqc|NN|_ tool|tool|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ from|from|IN|_ 3|3|CD|_ '|'|''|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ Cutadapt|cutadapt|JJ|_ v1|v1|NN|_ .10|.10|CD|_ ,|,|,|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 15|15|CD|_ nucleotides|nucleotide|NNS|_ .|.|.|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v1|v1|NN|_ .1.2|.1.2|CD|_ ,|,|,|_ by|by|IN|_ allowing|allow|VBG|_ up|up|RP|_ to|to|TO|_ 7|7|CD|_ mapping|mapping|NN|_ positions|position|NNS|_ to|to|TO|_ enable|enable|VB|_ mapping|map|VBG|_ to|to|TO|_ the|the|DT|_ 7|7|CD|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ parameters|parameter|NNS|_ :|:|:|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -|-|:|_ m|m|NN|_ 7|7|CD|_ -|-|:|_ a|a|DT|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ -5|-5|CD|_ 5|5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ rescaled|rescale|VBN|_ to|to|TO|_ a|a|DT|_ size|size|NN|_ of|of|IN|_ 10|10|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ BEDGraph|bedgraph|NN|_ files|file|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ genomeCoverageBed|genomecoveragebed|JJ|_ utility|utility|NN|_ of|of|IN|_ the|the|DT|_ BEDTools|bedtool|NNS|_ suite|suite|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ DMS-seq|dms-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pooled|JJ|_ Total|total|JJ|_ and|and|CC|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pooled|JJ|_ Total|total|JJ|_ and|and|CC|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ from|from|IN|_ both|both|DT|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ analyzed|analyze|VBN|_ transcript|transcript|NN|_ ,|,|,|_ 10|10|CD|_ files|file|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ SPET-seq|spet-seq|JJ|_ data|datum|NNS|_ for|for|IN|_ the|the|DT|_ 10|10|CD|_ transcription|transcription|NN|_ deciles|decile|NNS|_ are|be|VBP|_ provided|provide|VBN|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ http://www.rnaframework.com|http://www.rnaframework.com|NN|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ Count|count|NN|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ A|a|DT|_ file|file|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ each|each|DT|_ transcription|transcription|NN|_ intermediate|intermediate|NN|_ is|be|VBZ|_ provided|provide|VBN|_ .|.|.|_ For|for|IN|_ a|a|DT|_ detailed|detailed|JJ|_ description|description|NN|_ of|of|IN|_ the|the|DT|_ RC|rc|NN|_ format|format|NN|_ ,|,|,|_ please|please|VB|_ refer|refer|VB|_ to|to|TO|_ :|:|:|_ http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ|_
Each|each|DT|_ bacteria|bacterium|NNS|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ 25|25|CD|_ ml|ml|NN|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ homogeneously|homogeneously|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200|200|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|Buffer|NNP|_ A|A|NNP|_ -LSB-|-lsb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ Sucrose|sucrose|NN|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 50|50|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|buffer|NN|_ B|b|NN|_ -LSB-|-lsb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ;|;|:|_ 120|120|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ µl|µl|NN|_ Ready-Lyse|ready-lyse|NN|_ ™|™|CD|_ Lysozyme|Lysozyme|NNP|_ Solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ R1810M|r1810m|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ dropwise|dropwise|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ vial|vial|NN|_ was|be|VBD|_ gently|gently|RB|_ tilted|tilted|JJ|_ 5|5|CD|_ times|time|NNS|_ to|to|TO|_ ensure|ensure|VB|_ homogenous|homogenous|JJ|_ mixing|mix|VBG|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ 250|250|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|buffer|NN|_ C|c|NN|_ -LSB-|-lsb-|-LRB-|_ 0.5|0.5|CD|_ %|%|NN|_ Tween-20|tween-20|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ NaDOC|nadoc|NN|_ ;|;|:|_ 2|2|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ;|;|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ dropwise|dropwise|NN|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ At|at|IN|_ this|this|DT|_ stage|stage|NN|_ the|the|DT|_ solution|solution|NN|_ clears|clear|VBZ|_ considerably|considerably|RB|_ without|without|IN|_ increasing|increase|VBG|_ its|its|PRP$|_ viscosity|viscosity|NN|_ ,|,|,|_ and|and|CC|_ nucleoid|nucleoid|JJ|_ becomes|become|VBZ|_ visible|visible|JJ|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ cut|cut|NN|_ P1000|p1000|NN|_ pipette|pipette|NN|_ tip|tip|NN|_ ,|,|,|_ the|the|DT|_ whole|whole|JJ|_ sample|sample|NN|_ was|be|VBD|_ gently|gently|RB|_ layered|layer|VBN|_ on|on|IN|_ the|the|DT|_ top|top|NN|_ of|of|IN|_ a|a|DT|_ 5-30|5-30|CD|_ %|%|NN|_ w/v|w/v|NN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ -LSB-|-lsb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ 1|1|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP DTT|dtt|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 17,000|17,000|CD|_ RPM|rpm|NN|_ in|in|IN|_ a|a|DT|_ SW55Ti|sw55ti|NN|_ rotor|rotor|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 342194|342194|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 9|9|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ the|the|DT|_ nucleoid|nucleoid|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ syringe|syringe|NN|_ with|with|IN|_ a|a|DT|_ 18G|18g|NN|_ blunt|blunt|JJ|_ fill|fill|NN|_ needle|needle|NN|_ ,|,|,|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ new|new|JJ|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ .|.|.|_ The|the|DT|_ remaining|remain|VBG|_ gradient|gradient|NN|_ was|be|VBD|_ assumed|assume|VBN|_ to|to|TO|_ represent|represent|VB|_ the|the|DT|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ .|.|.|_ The|the|DT|_ nucleoid|nucleoid|NN|_ was|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ ml|ml|NN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 40|40|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 7.5|7.5|CD|_ ;|;|:|_ 150|150|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ;|;|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ;|;|:|_ 1|1|CD|_ mM|mm|NN|KWSUPP DTT|dtt|NN|_ ;|;|:|_ 0.01|0.01|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ pulse|pulse|NN|_ vortexed|vortex|VBD|_ for|for|IN|_ 5|5|CD|_ seconds|seconds|NNS|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 28,000|28,000|CD|_ RPM|rpm|NN|_ in|in|IN|_ a|a|DT|_ SW55Ti|sw55ti|NN|_ rotor|rotor|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ nucleoid|nucleoid|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ 2|2|CD|_ ml|ml|NN|_ of|of|IN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ ,|,|,|_ taking|take|VBG|_ care|care|NN|_ not|not|RB|_ to|to|TO|_ disturb|disturb|VB|_ it|it|PRP|_ .|.|.|_ The|the|DT|_ nucleoid|nucleoid|NN|_ was|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ µl|µl|NN|_ Wash|Wash|NNP|_ &|&|CC|_ Resuspension|Resuspension|NNP|_ buffer|buffer|NN|_ ,|,|,|_ and|and|CC|_ solubilized|solubilize|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 0.1|0.1|CD|_ gr|gr|NN|_ acid-washed|acid-washed|JJ|_ glass|glass|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ G1145|g1145|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ shaking|shake|VBG|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ in|in|IN|_ a|a|DT|_ TissueLyser|TissueLyser|NNP|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ each|each|DT|_ 100|100|CD|_ µl|µl|NN|_ of|of|IN|_ purified|purify|VBN|_ nucleoids|nucleoid|NNS|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TRIzol|trizol|NN|_ ®|®|CD|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 15596-018|15596-018|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ all|all|DT|_ experiments|experiment|NNS|_ ,|,|,|_ RNA|rna|NN|_ from|from|IN|_ cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -LRB-|-lrb-|-LRB-|_ corresponding|correspond|VBG|_ to|to|TO|_ mature|mature|JJ|_ RNA|rna|NN|_ species|species|NNS|_ -RRB-|-rrb-|-RRB-|_ had|have|VBD|_ RIN|RIN|NNP|_ >|>|JJR|_ 9.5|9.5|CD|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ yield|yield|NN|_ from|from|IN|_ nucleoid|nucleoid|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ ~|~|CD|_ 6|6|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ content|content|NN|_ .|.|.|_
10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ pre-adenylated|pre-adenylated|JJ|_ -LRB-|-lrb-|-LRB-|_ rApp|rapp|NN|_ -RRB-|-rrb-|-RRB-|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ nascent|nascent|JJ|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ mature|mature|JJ|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ in|in|IN|_ a|a|DT|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 20|20|CD|_ μl|μl|NN|_ ,|,|,|_ using|use|VBG|_ 400|400|CD|_ U|U|NNP|_ T4|t4|NN|_ RNA|rna|NN|_ Ligase|ligase|NN|_ 2|2|CD|_ ,|,|,|_ Deletion|deletion|NN|_ Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ LR2D11310K|lr2d11310k|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20|20|CD|_ %|%|NN|_ PEG-8000|peg-8000|NN|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ Fragmentation|fragmentation|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 65|65|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.3|8.3|CD|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ;|;|:|_ 5|5|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragment|VBN|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ in|in|IN|_ 5.5|5.5|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ heat-denatured|heat-denatured|JJ|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ volume|volume|NN|_ of|of|IN|_ 10|10|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP dNTPs|dntp|NNS|_ ,|,|,|_ 5|5|CD|_ pmol|pmol|NN|_ of|of|IN|_ RT|rt|NN|_ primer|primer|NN|_ ,|,|,|_ 20|20|CD|_ U|U|NNP|_ RNaseOUT|RNaseOUT|NNP|_ ™|™|NNP|_ Recombinant|recombinant|JJ|_ Ribonuclease|ribonuclease|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 10777-019|10777-019|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ SuperScript|SuperScript|NNP|_ ®|®|SYM|_ III|iii|CD|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 18080-044|18080-044|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 50|50|CD|_ °C|°c|NN|_ for|for|IN|_ 50|50|CD|_ minutes|minute|NNS|_ .|.|.|_ Template|template|NN|_ RNA|rna|NN|_ was|be|VBD|_ degraded|degrade|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ μl|μl|NN|_ of|of|IN|_ 1|1|CD|_ M|m|NN|_ NaOH|naoh|NN|_ ,|,|,|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 6|6|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ resolved|resolve|VBN|_ on|on|IN|_ a|a|DT|_ 10|10|CD|_ %|%|NN|_ TBE-Urea|tbe-urea|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ gel|gel|NN|_ slice|slice|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ fragments|fragment|NNS|_ in|in|IN|_ the|the|DT|_ range|range|NN|_ 40-150|40-150|CD|_ nt|nt|NN|_ was|be|VBD|_ cut|cut|VBN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ passive|passive|NN|_ diffusion|diffusion|NN|_ in|in|IN|_ Diffusion|Diffusion|NNP|_ buffer|buffer|NN|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ moderate|moderate|JJ|_ shaking|shake|VBG|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ ml|ml|NN|_ Isopropanol|isopropanol|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ μl|μl|NN|_ Glycogen|glycogen|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ μg/μl|μg/μl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 8.25|8.25|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ 10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ phosphorylated|phosphorylate|VBN|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ -|-|:|_ OH|oh|NN|_ of|of|IN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.05|0.05|CD|_ mM|mm|NN|KWSUPP ATP|atp|NN|SUPP ,|,|,|_ 20|20|CD|_ %|%|NN|_ PEG-4000|peg-4000|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ CircLigase|CircLigase|NNP|_ ™|™|NNP|_ II|II|NNP|_ ssDNA|ssDNA|NNP|_ Ligase|Ligase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ CL9025K|cl9025k|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 60|60|CD|_ °C|°c|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ ,|,|,|_ and|and|CC|_ 68|68|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ excess|excess|JJ|_ adapter|adapter|NN|_ using|use|VBG|_ 1.8|1.8|CD|_ volumes|volume|NNS|_ of|of|IN|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ A63881|a63881|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ ,|,|,|_ and|and|CC|_ indexed|index|VBD|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ introduced|introduce|VBN|_ by|by|IN|_ 15|15|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 25|25|CD|_ pmol|pmol|NN|_ of|of|IN|_ each|each|DT|_ primer|primer|NN|_ ,|,|,|_ and|and|CC|_ 25|25|CD|_ μl|μl|NN|_ NEBNext|nebnext|NN|_ ®|®|CD|_ High-Fidelity|high-fidelity|NN|_ 2X|2x|NN|_ PCR|pcr|NN|_ Master|master|NN|_ Mix|Mix|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ M0541L|m0541l|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Nucleoid|nucleoid|NN|_ fraction|fraction|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
substr|substr|NN|_ :|:|:|_ MG1655|mg1655|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ Nucleoid|nucleoid|NN|_ fraction|fraction|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Nucleoid|nucleoid|NN|_ fraction|fraction|NN|_
Danny|Danny|NNP|_ ,|,|,|_ ,|,|,|_ Incarnato|Incarnato|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t0|t0|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t10|t10|CD|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t30|t30|CD|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t60|t60|CD|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t10|t10|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t30|t30|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t60|t60|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t10|t10|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t30|t30|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t60|t60|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t0|t0|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t10|t10|CD|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t30|t30|CD|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t60|t60|CD|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t10|t10|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t30|t30|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t60|t60|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t10|t10|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t30|t30|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t60|t60|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t0|t0|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t10|t10|CD|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t30|t30|CD|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t60|t60|CD|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t10|t10|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t30|t30|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t60|t60|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t10|t10|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t30|t30|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https://galaxyproject.org|https://galaxyproject.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ FASTX|fastx|NN|_ tools|tool|NNS|_ in|in|IN|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ by|by|IN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ 80|80|CD|_ %|%|NN|_ of|of|IN|_ sequence|sequence|NN|_ >|>|JJR|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ at|at|IN|_ both|both|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ a|a|DT|_ window|window|NN|_ and|and|CC|_ step|step|NN|_ size|size|NN|_ of|of|IN|_ 1|1|CD|_ with|with|IN|_ quality|quality|NN|_ score|score|NN|_ >|>|JJR|_ 20|20|CD|_ .|.|.|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ tabulated|tabulate|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ SAM|SAM|NNP|_ alignment|alignment|NN|_ files|file|NNS|_ using|use|VBG|_ the|the|DT|_ HTSeq-count|htseq-count|JJ|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ intersection|intersection|NN|_ non-empty|non-empty|JJ|_ mode|mode|NN|_ .|.|.|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t60|t60|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg/L|mg/l|NN|_ uracil|uracil|NN|SUPP and|and|CC|_ 500|500|CD|_ µg/L|µg/l|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ which|which|WDT|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 18|18|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ starter|starter|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:30|1:30|CD|_ to|to|TO|_ initiate|initiate|VB|_ the|the|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ and|and|CC|_ divided|divide|VBN|_ into|into|IN|_ three|three|CD|_ 500|500|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ NM3|nm3|NN|_ in|in|IN|_ each|each|DT|_ ,|,|,|_ which|which|WDT|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
Stephen|Stephen|NNP|_ ,|,|,|_ Patrick|Patrick|NNP|_ ,|,|,|_ LaVoie|LaVoie|NNP|_
Basecalls|Basecalls|NNPS|_ performed|perform|VBD|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ CP009273|CP009273|NNP|_ .1|.1|CD|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_
Quantification|quantification|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ and|and|CC|_ analysis|analysis|NN|_ of|of|IN|_ gene|gene|NN|_ differential|differential|JJ|_ expression|expression|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Fragment|fragment|NN|_ Per|per|IN|_ Kilo|Kilo|NNP|_ bases|basis|NNS|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ value|value|NN|_ based|base|VBN|_ rsem|rsem|NN|_ software|software|NN|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ and|and|CC|_ edgeR|edger|NN|_ version|version|NN|_ 3.4.2|3.4.2|CD|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP009273|cp009273|NN|_ .1|.1|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Excel|Excel|NNP|_ file|file|NN|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ of|of|IN|_ different|different|JJ|_ genes|gene|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ clean-up|clean-up|JJ|_ and|and|CC|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ with|with|IN|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #FC|#fc|NN|_ -122-1001|-122-1001|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacteria|bacterium|NNS|_ cells|cell|NNS|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
product|product|NN|_ :|:|:|_ Butanol|Butanol|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Bacteria|bacterium|NNS|_ cells|cell|NNS|_
Chunhua|Chunhua|NNP|_ ,|,|,|_ ,|,|,|_ Zhao|Zhao|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
AR1|ar1|NN|_ -|-|:|_ /|/|:|_ AR2|ar2|SYM|_ -|-|:|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ AR1|ar1|NN|_ -|-|:|_ /|/|:|_ AR2|ar2|SYM|_ -|-|:|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
AR1|ar1|NN|_ -|-|:|_ /|/|:|_ AR2|ar2|SYM|_ -|-|:|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
AR1|ar1|NN|_ -|-|:|_ /|/|:|_ AR2|ar2|SYM|_ -|-|:|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ AR1|ar1|NN|_ -|-|:|_ /|/|:|_ AR2|ar2|SYM|_ -|-|:|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
AR1|ar1|NN|_ -|-|:|_ /|/|:|_ AR2|ar2|SYM|_ -|-|:|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ WT|wt|JJ|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ WT|wt|JJ|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ WT|wt|JJ|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ WT|wt|JJ|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ WT|wt|JJ|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ WT|WT|NNP|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
WT|wt|JJ|_ WT|wt|JJ|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100Q|k100q|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ K100Q|k100q|NN|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100Q|k100q|NN|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100Q|k100q|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ K100Q|k100q|NN|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100Q|k100q|NN|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100Q|k100q|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ K100Q|k100q|NN|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100Q|k100q|NN|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100R|k100r|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ K100R|k100r|NN|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100R|k100r|NN|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100R|k100r|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ K100R|k100r|NN|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100R|k100r|NN|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
Base|Base|NNP|_ calls|call|VBZ|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Cell|Cell|NNP|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100R|k100r|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
genotype/variation|genotype/variation|NN|_ :|:|:|_ K100R|k100r|NN|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential/Early|exponential/early|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD|od|JJ|_ ~|~|NN|_ 1.8|1.8|CD|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K100R|k100r|NN|_
Alan|Alan|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Wolfe|Wolfe|NNP|_
50|50|CD|_ bp|bp|NN|_ single-end|single-end|JJ|_ reads|read|VBZ|_ ,|,|,|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ with|with|IN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_ Alignments|alignment|NNS|_ with|with|IN|_ bowtie2|bowtie2|NN|_ mapping|map|VBG|_ quality|quality|NN|_ values|value|NNS|_ lower|lower|JJR|_ than|than|IN|_ 40|40|CD|_ were|be|VBD|_ not|not|RB|_ retained|retain|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ ,|,|,|_ leaving|leave|VBG|_ 128,413,654|128,413,654|CD|_ and|and|CC|_ 76,508,335|76,508,335|CD|_ reads|read|VBZ|_ .|.|.|_
In|in|IN|_ order|order|NN|_ to|to|TO|_ distinguish|distinguish|VB|_ between|between|IN|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ of|of|IN|_ transient|transient|JJ|_ products|product|NNS|_ of|of|IN|_ RNA|rna|NN|_ metabolism|metabolism|NN|_ and|and|CC|_ stable|stable|JJ|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ ,|,|,|_ we|we|PRP|_ developed|develop|VBD|_ an|a|DT|_ algorithm|algorithm|NN|_ to|to|TO|_ call|call|VB|_ coverage|coverage|NN|_ peaks|peak|NNS|_ .|.|.|_ The|the|DT|_ algorithm|algorithm|NN|_ will|will|MD|_ be|be|VB|_ discussed|discuss|VBN|_ in|in|IN|_ detail|detail|NN|_ in|in|IN|_ an|a|DT|_ upcoming|upcoming|JJ|_ manuscript|manuscript|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ scripts|script|NNS|_ used|use|VBN|_ are|be|VBP|_ available|available|JJ|_ upon|upon|IN|_ request|request|NN|_ from|from|IN|_ the|the|DT|_ authors|author|NNS|_ .|.|.|_ In|in|IN|_ short|short|RB|_ ,|,|,|_ positions|position|NNS|_ in|in|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ considered|consider|VBN|_ in|in|IN|_ descending|descend|VBG|_ order|order|NN|_ of|of|IN|_ coverage|coverage|NN|_ and|and|CC|_ assigned|assign|VBN|_ a|a|DT|_ p-value|p-value|NN|_ based|base|VBN|_ on|on|IN|_ a|a|DT|_ Poisson|Poisson|NNP|_ distribution|distribution|NN|_ parameterized|parameterize|VBN|_ by|by|IN|_ the|the|DT|_ mean|mean|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ covered|cover|VBN|_ bases|basis|NNS|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_ Peaks|peak|NNS|_ were|be|VBD|_ rejected|reject|VBN|_ if|if|IN|_ their|they|PRP$|_ p-values|p-value|NNS|_ exceeded|exceed|VBD|_ 1e-4|1e-4|NN|_ or|or|CC|_ if|if|IN|_ there|there|EX|_ existed|exist|VBD|_ a|a|DT|_ >|>|JJR|_ 10-bp|10-bp|JJ|_ window|window|NN|_ containing|contain|VBG|_ the|the|DT|_ peak|peak|NN|_ in|in|IN|_ which|which|WDT|_ all|all|DT|_ positions|position|NNS|_ were|be|VBD|_ within|within|IN|_ 2-fold|2-fold|JJ|_ coverage|coverage|NN|_ of|of|IN|_ the|the|DT|_ peak|peak|JJ|_ position|position|NN|_ .|.|.|_ Parameters|parameter|NNS|_ were|be|VBD|_ chosen|choose|VBN|_ based|base|VBN|_ on|on|IN|_ analysis|analysis|NN|_ of|of|IN|_ annotated|annotated|JJ|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ qualitative|qualitative|JJ|_ analysis|analysis|NN|_ of|of|IN|_ peaks|peak|NNS|_ .|.|.|_ This|this|DT|_ resulted|result|VBD|_ in|in|IN|_ 20,019|20,019|CD|_ peaks|peak|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ GFF|gff|NN|_ file|file|NN|_ containing|contain|VBG|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ annotations|annotation|NNS|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BIGWIG|bigwig|NN|_ file|file|NN|_ containing|contain|VBG|_ coverage|coverage|NN|_ tracks|track|NNS|_ from|from|IN|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ RACE|race|NN|_ data|datum|NNS|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ -LRB-|-lrb-|-LRB-|_ Lybecker|Lybecker|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
total|total|VBP|_ DNaseI|dnasei|NN|_ treated|treated|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ RNA|rna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ RNA|rna|NN|_ adapter|adapter|NN|_ ,|,|,|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ multiplexing|multiplex|VBG|_ adapter|adapter|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Oligonucleotide|oligonucleotide|NN|_ sequences|sequence|NNS|_ ©|©|SYM|_ 2007-2014|2007-2014|CD|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ .|.|.|_ All|all|DT|_ rights|rights|NNS|_ reserved|reserve|VBN|_ -RRB-|-rrb-|-RRB-|_ blocked|block|VBD|_ at|at|IN|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ with|with|IN|_ an|a|DT|_ inverted|inverted|JJ|_ dT|dt|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ GAUCGGAAGAGCACACGUCU|gaucggaagagcacacgucu|NN|_ -LSB-|-lsb-|-LRB-|_ idT|idt|NN|_ -RSB-|-rsb-|-RRB-|_ -3|-3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ at|at|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ end|end|NN|_ using|use|VBG|_ T4|t4|NN|_ PNK|pnk|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ RNA|rna|NN|_ adapter|adapter|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ of|of|IN|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ using|use|VBG|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 1.5|1.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 20|20|CD|_ °C|°c|NN|_ for|for|IN|_ 6|6|CD|_ hours|hour|NNS|_ in|in|IN|_ 1X|1x|NN|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ reaction|reaction|NN|_ buffer|buffer|NN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP ATP|atp|NN|SUPP ,|,|,|_ 30|30|CD|_ µM|µm|NN|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ RNA|rna|NN|_ adapter|adapter|NN|_ ,|,|,|_ 10|10|CD|_ %|%|NN|_ DMSO|dmso|NN|_ ,|,|,|_ 10|10|CD|_ U|u|NN|_ of|of|IN|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ I|I|PRP|_ ,|,|,|_ and|and|CC|_ 40|40|CD|_ U|u|NN|_ of|of|IN|_ RNasin|rnasin|NN|_ -LRB-|-lrb-|-LRB-|_ Promega|promega|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ reaction|reaction|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ in|in|IN|_ equivalents|equivalent|NNS|_ of|of|IN|_ 100|100|CD|_ ng|ng|NN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ fragmentation|fragmentation|NN|_ reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ®|®|NNP|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ and|and|CC|_ subsequently|subsequently|RB|_ phosphorylated|phosphorylate|VBN|_ at|at|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ ends|end|VBZ|_ using|use|VBG|_ T4|t4|NN|_ PNK|pnk|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ allow|allow|VB|_ for|for|IN|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adapter|adapter|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ size-selected|size-selected|JJ|_ -LRB-|-lrb-|-LRB-|_ ≈|≈|JJ|_ 150-300|150-300|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ purified|purify|VBN|_ over|over|IN|_ a|a|DT|_ denaturing|denature|VBG|_ 8|8|CD|_ %|%|NN|_ polyacrylamide/8|polyacrylamide/8|CD|_ M|m|NN|_ urea/TBE|urea/tbe|NN|_ gel|gel|NN|_ .|.|.|_ Gel|gel|NN|_ slices|slice|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ RNA|rna|NN|_ elution|elution|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.5|7.5|CD|_ ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 0.3|0.3|CD|_ M|m|NN|_ NaOAc|naoac|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ vigorous|vigorous|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ subsequently|subsequently|RB|_ ethanol|ethanol|NN|_ precipitated|precipitate|VBD|_ using|use|VBG|_ glycogen|glycogen|NN|_ as|as|IN|_ a|a|DT|_ carrier|carrier|NN|_ molecule|molecule|NN|_ .|.|.|_ The|the|DT|_ Illumina|Illumina|NNP|_ small|small|JJ|_ RNA|rna|NN|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ GUUCAGAGUUCUACAGUCCGACGAUC-3|guucagaguucuacaguccgacgauc-3|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ RNA|rna|NN|_ as|as|IN|_ described|describe|VBN|_ before|before|IN|_ except|except|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ adapter|adapter|NN|_ was|be|VBD|_ 52|52|CD|_ mM|mm|NN|KWSUPP and|and|CC|_ 20|20|CD|_ U|u|NN|_ of|of|IN|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ I|I|PRP|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ µl|µl|NN|_ .|.|.|_ The|the|DT|_ ligated|ligate|VBN|_ RNAs|rna|NNS|_ were|be|VBD|_ size-selected|size-selected|JJ|_ -LRB-|-lrb-|-LRB-|_ ≈|≈|JJ|_ 200-300|200-300|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ gel-purified|gel-purified|JJ|_ over|over|IN|_ a|a|DT|_ denaturing|denature|VBG|_ 8|8|CD|_ %|%|NN|_ polyacrylamide/8|polyacrylamide/8|CD|_ M|m|NN|_ urea/TBE|urea/tbe|NN|_ gel|gel|NN|_ -LRB-|-lrb-|-LRB-|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ di-tagged|di-tagged|JJ|_ RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ reverse-transcribed|reverse-transcribed|JJ|_ with|with|IN|_ SuperScript|SuperScript|NNP|_ ®|®|NNP|_ II|II|NNP|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ random|random|JJ|_ nonamers|nonamer|NNS|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RNase|rnase|NN|_ H|h|NN|_ -LRB-|-lrb-|-LRB-|_ Promega|promega|NN|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ and|and|CC|_ cDNA|cdna|NN|_ was|be|VBD|_ amplified|amplify|VBN|_ in|in|IN|_ PCR|pcr|NN|_ carried|carry|VBD|_ out|out|RP|_ using|use|VBG|_ Phusion|Phusion|NNP|_ ®|®|SYM|_ High-Fidelity|High-Fidelity|NNP|_ Polymerase|Polymerase|NNP|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ amplified|amplify|VBN|_ with|with|IN|_ modified|modify|VBN|_ designed|design|VBN|_ Illumina-compatible|illumina-compatible|JJ|_ PCR|pcr|NN|_ primers|primer|NNS|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ '|'|''|_ library|library|NN|_ Forward|forward|RB|_ 5|5|CD|_ '|'|''|_ -|-|:|_ CAAGCAGAAGACGGCATACGACAGGTTCAGAGTTCTACAGTCCGA-3|caagcagaagacggcatacgacaggttcagagttctacagtccga-3|NN|_ '|'|''|_ ;|;|:|_ Reverse|reverse|JJ|_ 5|5|CD|_ '|'|''|_ -|-|:|_ AATGATACGGCGACCACCGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3|aatgatacggcgaccaccgagatgtgactggagttcagacgtgtgctcttccgatc-3|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ 18|18|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ The|the|DT|_ products|product|NNS|_ were|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ analyzed|analyze|VBN|_ on|on|IN|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ 3|3|CD|_ '|'|''|_ end|end|NN|_ enriched|enriched|JJ|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ individual|individual|JJ|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ IIx|IIx|NNP|_ lanes|lane|NNS|_ -LRB-|-lrb-|-LRB-|_ 36|36|CD|_ bp|bp|NN|_ ,|,|,|_ single-end|single-end|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ on|on|IN|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ lanes|lane|NNS|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ bp|bp|NN|_ ,|,|,|_ single-end|single-end|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ primer|primer|NN|_ based|base|VBN|_ on|on|IN|_ Illumina|Illumina|NNP|_ Multiplexing|Multiplexing|NNP|_ Read|Read|NNP|_ 2|2|CD|_ Sequencing|sequencing|NN|_ Primer|primer|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ '|'|''|_ -|-|:|_ GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3|gtgactggagttcagacgtgtgctcttccgatc-3|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ the|the|DT|_ CSF|csf|NN|_ NGS|ngs|NN|_ unit|unit|NN|_ http://csf.ac.at/|http://csf.ac.at/|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Philipp|philipp|NN|_ ,|,|,|_ ,|,|,|_ Rescheneder|Rescheneder|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -LSB-|-lsb-|-LRB-|_ linebreak|linebreak|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Individual|individual|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg/mL|μg/ml|NN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ Gold|gold|NN|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ MO|MO|NNP|_ ,|,|,|_ K-120-5|k-120-5|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ grown|grow|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 1000|1000|CD|_ RPM|RPM|NNP|_ in|in|IN|_ V-bottom|V-bottom|NNP|_ 96-well|96-well|JJ|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ Nunc|Nunc|NNP|_ ,|,|,|_ Roskilde|Roskilde|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ ,|,|,|_ 249952|249952|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ an|a|DT|_ ELMI|ELMI|NNP|_ Digital|Digital|NNP|_ Thermos|Thermos|NNP|_ Microplates|Microplates|NNP|_ shaker|shaker|NN|_ incubator|incubator|NN|_ -LRB-|-lrb-|-LRB-|_ Elmi|Elmi|NNP|_ Ltd|Ltd|NNP|_ ,|,|,|_ Riga|Riga|NNP|_ ,|,|,|_ Latvia|Latvia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ day|day|NN|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 178-fold|178-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ two|two|CD|_ serial|serial|JJ|_ dilutions|dilution|NNS|_ of|of|IN|_ 15|15|CD|_ µL|µl|NN|_ into|into|IN|_ 185|185|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ ELMI|elmi|NN|_ shaker|shaker|NN|_ incubator|incubator|NN|_ conditions|condition|NNS|_ for|for|IN|_ three|three|CD|_ hours|hour|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 4.56|4.56|CD|_ µL|µl|NN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ culture|culture|NN|_ tubes|tube|NNS|_ -LRB-|-lrb-|-LRB-|_ Falcon|Falcon|NNP|_ 14|14|CD|_ mL|ml|NN|_ round-bottom|round-bottom|JJ|_ polypropylene|polypropylene|NN|_ tubes|tube|NNS|_ ;|;|:|_ Corning|Corning|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ 352059|352059|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ For|for|IN|_ Erlenmeyer|Erlenmeyer|NNP|_ flask|flask|NN|_ assays|assay|NNS|_ -LRB-|-lrb-|-LRB-|_ Pyrex|pyrex|NN|_ 250|250|CD|_ mL|ml|NN|_ ;|;|:|_ Cole-Palmer|Cole-Palmer|NNP|_ ,|,|,|_ IL|il|NN|_ ,|,|,|_ 4980-250|4980-250|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 658-fold|658-fold|JJ|_ -LRB-|-lrb-|-LRB-|_ 76|76|CD|_ µL|µl|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ glycerol|glycerol|NN|SUPP with|with|IN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ inducers|inducer|NNS|_ .|.|.|_ Eight|eight|CD|_ inducer|inducer|NN|_ combinations|combination|NNS|_ were|be|VBD|_ used|use|VBN|_ that|that|IN|_ cover|cover|VBP|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ ,|,|,|_ 10|10|CD|_ ng/mL|ng/ml|NN|_ aTc|atc|NN|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ mM|mm|NN|KWSUPP L-arabinose|l-arabinose|NN|_ .|.|.|_ Culture|culture|NN|_ tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ Innova|Innova|NNP|_ 44|44|CD|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ ,|,|,|_ CT|ct|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ five|five|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Thomas|Thomas|NNP|_ ,|,|,|_ Edward|Edward|NNP|_ ,|,|,|_ Gorochowski|Gorochowski|NNP|_